#work_resolve-deepTools-issues.md
- Get situated
- Align the datasets
- Correct chromosome names in
S288C_reference_sequence_R64-3-1_20210421.fa
Code: Get situated
#!/bin/bash
p_data="${HOME}/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802"
p_rename="${p_data}/renamed"
if [[ ! -d "${p_rename}" ]]; then mkdir -p "${p_rename}"; fi
typeset -A data=(
["${p_data}/SRR7175375.fastq"]="${p_rename}/Brn1_Q_rep1_ChIP.fastq"
["${p_data}/SRR7175376.fastq"]="${p_rename}/Brn1_Q_rep1_input.fastq"
["${p_data}/SRR7175377.fastq"]="${p_rename}/Brn1_Q_rep2_ChIP.fastq"
["${p_data}/SRR7175378.fastq"]="${p_rename}/Brn1_Q_rep2_input.fastq"
["${p_data}/SRR7175379.fastq"]="${p_rename}/Brn1_Q_rep3_ChIP.fastq"
["${p_data}/SRR7175380.fastq"]="${p_rename}/Brn1_Q_rep3_input.fastq"
["${p_data}/SRR7175382.fastq"]="${p_rename}/Brn1_Q_all_input.fastq"
["${p_data}/SRR7175381.fastq"]="${p_rename}/Brn1_Q_all_ChIP.fastq"
["${p_data}/SRR7175367.fastq"]="${p_rename}/Brn1_log_rep1_ChIP.fastq"
["${p_data}/SRR7175368.fastq"]="${p_rename}/Brn1_log_rep1_input.fastq"
["${p_data}/SRR7175369.fastq"]="${p_rename}/Brn1_log_rep2_ChIP.fastq"
["${p_data}/SRR7175370.fastq"]="${p_rename}/Brn1_log_rep2_input.fastq"
["${p_data}/SRR7175371.fastq"]="${p_rename}/Brn1_log_rep3_ChIP.fastq"
["${p_data}/SRR7175372.fastq"]="${p_rename}/Brn1_log_rep3_input.fastq"
["${p_data}/SRR7175373.fastq"]="${p_rename}/Brn1_log_all_ChIP.fastq"
["${p_data}/SRR7175374.fastq"]="${p_rename}/Brn1_log_all_input.fastq"
)
# Rather than rename the initial files, make "symbolic links" to the files
#+ with new, better-detailed names
for i in "${!data[@]}"; do
echo """
key: ${i}
value: ${data[${i}]}
"""
ln -s "${i}" "${data["${i}"]}"
doneCode: Submit job to make bowtie2 indices for S288C R64-3-1
#!/bin/bash
source activate coverage_env
which bowtie2-build
bowtie2-build --help
job_name="bowtie2-build" # echo "${job_name}"
threads=8 # echo "${threads}"
d_genome="${HOME}/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421" # ., "${d_genome}"
f_genome="${d_genome}/fasta/S288C_reference_sequence_R64-3-1_20210421.fa" # ., "${f_genome}"
o_indices="${d_genome}/bowtie2/$(basename "${f_genome}" .fa)" # echo "${o_indices}"
sh_err_out="$(dirname "${d_genome}/bowtie2/$(basename "${f_genome}" .fa)")/sh_err_out" # echo "${sh_err_out}"
if [[ ! -d "${d_genome}/bowtie2" ]]; then mkdir -p "${d_genome}/bowtie2/sh_err_out"; fi
echo """
sbatch \\
--job-name=${job_name} \\
--nodes=1 \\
--cpus-per-task=${threads} \\
--error=${sh_err_out}/${job_name}.%A.stderr.txt \\
--output=${sh_err_out}/${job_name}.%A.stdout.txt \\
bowtie2-build \\
--threads ${threads} \\
${f_genome} \\
${o_indices} \\
> >(tee -a ${sh_err_out}/${job_name}.stdout.txt) \\
2> >(tee -a ${sh_err_out}/${job_name}.stderr.txt)
"""
if [[ -f "${sh_err_out}/${job_name}.sh" ]]; then
rm "${sh_err_out}/${job_name}.sh"
fi
cat << script > "${sh_err_out}/${job_name}.sh"
#!/bin/bash
#SBATCH --job-name=${job_name}
#SBATCH --nodes=1
#SBATCH --cpus-per-task=${threads}
#SBATCH --error=${sh_err_out}/${job_name}.%A.stderr.txt
#SBATCH --output=${sh_err_out}/${job_name}.%A.stdout.txt
# ${job_name}.sh
# KA
# $(date '+%Y-%m%d')
eval "\$(conda shell.bash hook)"
source activate coverage_env
bowtie2-build \\
--threads ${threads} \\
${f_genome} \\
${o_indices}
script
# cat "${sh_err_out}/${job_name}.sh"
sbatch "${sh_err_out}/${job_name}.sh"Printed: Submit job to make bowtie2 indices for S288C R64-3-1
❯ source activate coverage_env
❯ which bowtie2-build
/home/kalavatt/miniconda3/envs/coverage_env/bin/bowtie2-build
❯ bowtie2-build --help
Bowtie 2 version 2.5.1 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea)
Usage: bowtie2-build [options]* <reference_in> <bt2_index_base>
reference_in comma-separated list of files with ref sequences
bt2_index_base write bt2 data to files with this dir/basename
*** Bowtie 2 indexes will work with Bowtie v1.2.3 and later. ***
Options:
-f reference files are Fasta (default)
-c reference sequences given on cmd line (as
<reference_in>)
--large-index force generated index to be 'large', even if ref
has fewer than 4 billion nucleotides
--debug use the debug binary; slower, assertions enabled
--sanitized use sanitized binary; slower, uses ASan and/or UBSan
--verbose log the issued command
-a/--noauto disable automatic -p/--bmax/--dcv memory-fitting
-p/--packed use packed strings internally; slower, less memory
--bmax <int> max bucket sz for blockwise suffix-array builder
--bmaxdivn <int> max bucket sz as divisor of ref len (default: 4)
--dcv <int> diff-cover period for blockwise (default: 1024)
--nodc disable diff-cover (algorithm becomes quadratic)
-r/--noref don't build .3/.4 index files
-3/--justref just build .3/.4 index files
-o/--offrate <int> SA is sampled every 2^<int> BWT chars (default: 5)
-t/--ftabchars <int> # of chars consumed in initial lookup (default: 10)
--threads <int> # of threads
--seed <int> seed for random number generator
-q/--quiet verbose output (for debugging)
--h/--help print this message and quit
--version print version information and quit
❯ if [[ ! -d "${d_genome}/bowtie2" ]]; then mkdir -p "${d_genome}/bowtie2/sh_err_out"; fi
mkdir: created directory '/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2'
mkdir: created directory '/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/sh_err_out'
❯ echo """
> sbatch \\
> --job-name=${job_name} \\
> --nodes=1 \\
> --cpus-per-task=${threads} \\
> --error=${sh_err_out}/${job_name}.%A.stderr.txt \\
> --output=${sh_err_out}/${job_name}.%A.stdout.txt \\
> bowtie2-build \\
> --threads ${threads} \\
> ${f_genome} \\
> ${o_indices} \\
> > >(tee -a ${sh_err_out}/${job_name}.stdout.txt) \\
> 2> >(tee -a ${sh_err_out}/${job_name}.stderr.txt)
> """
sbatch \
--job-name=bowtie2-build \
--nodes=1 \
--cpus-per-task=8 \
--error=/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/sh_err_out/bowtie2-build.%A.stderr.txt \
--output=/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/sh_err_out/bowtie2-build.%A.stdout.txt \
bowtie2-build \
--threads 8 \
/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa \
/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/sh_err_out/bowtie2-build.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/sh_err_out/bowtie2-build.stderr.txt)
❯ cat << script > "${sh_err_out}/${job_name}.sh"
> #!/bin/bash
>
> #SBATCH --job-name=${job_name}
> #SBATCH --nodes=1
> #SBATCH --cpus-per-task=${threads}
> #SBATCH --error=${sh_err_out}/${job_name}.%A.stderr.txt
> #SBATCH --output=${sh_err_out}/${job_name}.%A.stdout.txt
>
> # ${job_name}.sh
> # KA
> # $(date '+%Y-%m%d')
>
> eval "\$(conda shell.bash hook)"
> source activate coverage_env
>
> bowtie2-build \\
> --threads ${threads} \\
> ${f_genome} \\
> ${o_indices}
> script
❯ cat "${sh_err_out}/${job_name}.sh"
#!/bin/bash
#SBATCH --job-name=bowtie2-build
#SBATCH --nodes=1
#SBATCH --cpus-per-task=8
#SBATCH --error=/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/sh_err_out/bowtie2-build.%A.stderr.txt
#SBATCH --output=/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/sh_err_out/bowtie2-build.%A.stdout.txt
# bowtie2-build.sh
# KA
# 2023-0406
eval "$(conda shell.bash hook)"
source activate coverage_env
bowtie2-build \
--threads 8 \
/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa \
/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421Code: Run bowtie2 alignment
#!/bin/bash
tmux new -s align
grabnode # 16 cores, defaults
source activate coverage_env
which bowtie2
bowtie2 --help
d_work="${HOME}/tsukiyamalab/Kris/2023_rDNA/results" # ., "${d_work}"
if [[ ! -d "${d_work}/2023-0406" ]]; then
mkdir -p "${d_work}/2023-0406/bams/err_out"
fi
cd "${d_work}"
pwd
threads="${SLURM_CPUS_ON_NODE}" # echo "${threads}"
d_genome="${HOME}/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421" # ., "${d_genome}"
f_genome="${d_genome}/fasta/S288C_reference_sequence_R64-3-1_20210421.fa" # ., "${f_genome}"
f_indices="${d_genome}/bowtie2/$(basename "${f_genome}" .fa)" # ., "${f_indices}"*
err_out="${d_work}/2023-0406/bams/err_out" # ., "${err_out}"
d_bams="$(dirname ${err_out})"
p_data="${HOME}/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed"
unset fastqs
typeset -a fastqs=(
"${p_data}/Brn1_Q_rep1_ChIP.fastq"
"${p_data}/Brn1_Q_rep1_input.fastq"
"${p_data}/Brn1_Q_rep2_ChIP.fastq"
"${p_data}/Brn1_Q_rep2_input.fastq"
"${p_data}/Brn1_Q_rep3_ChIP.fastq"
"${p_data}/Brn1_Q_rep3_input.fastq"
"${p_data}/Brn1_Q_all_input.fastq"
"${p_data}/Brn1_Q_all_ChIP.fastq"
"${p_data}/Brn1_log_rep1_ChIP.fastq"
"${p_data}/Brn1_log_rep1_input.fastq"
"${p_data}/Brn1_log_rep2_ChIP.fastq"
"${p_data}/Brn1_log_rep2_input.fastq"
"${p_data}/Brn1_log_rep3_ChIP.fastq"
"${p_data}/Brn1_log_rep3_input.fastq"
"${p_data}/Brn1_log_all_ChIP.fastq"
"${p_data}/Brn1_log_all_input.fastq"
)
for i in "${fastqs[@]}"; do ., "${i}"; done
for i in "${fastqs[@]}"; do
# i="${fastqs[0]}" # echo "${i}"
# echo """
# bowtie2 \\
# -p ${threads} \\
# --very-sensitive-local \\
# -x ${f_indices} \\
# -U ${i} \\
# | samtools sort \\
# -@ ${threads} \\
# -l 0 \\
# -O bam \\
# | samtools view \\
# -@ ${threads} \\
# -O bam \\
# -o ${i%.fastq}.bam \\
# > >(tee -a ${err_out}/bowtie2_samtools-sort_samtools-view.stdout.txt) \\
# 2> >(tee -a ${err_out}/bowtie2_samtools-sort_samtools-view.stderr.txt)
# """
in_fastq="${i}" # ., "${in_fastq}"
out_bam="${d_bams}/$(basename "${in_fastq}" .fastq).bam" # echo "${out_bam}"
echo "#### $(basename ${in_fastq}) ####"
{
bowtie2 \
-p "${threads}" \
--very-sensitive-local \
-x "${f_indices}" \
-U "${in_fastq}" \
| samtools sort \
-@ "${threads}" \
-l 0 \
-O "bam" \
| samtools view \
-@ "${threads}" \
-O "bam" \
-o "${out_bam}"
} \
>> >(tee -a ${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort_samtools-view.stdout.txt) \
2>> >(tee -a ${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort_samtools-view.stderr.txt)
echo ""
if [[ -f "${out_bam}" ]]; then
samtools index \
-@ "${threads}" \
"${out_bam}" \
> >(tee -a ${err_out}/$(basename "${out_bam}" .bam).samtools-index.stdout.txt) \
2> >(tee -a ${err_out}/$(basename "${out_bam}" .bam).samtools-index.stderr.txt)
fi
echo ""
donePrinted: Run bowtie2 alignment
❯ which bowtie2
/home/kalavatt/miniconda3/envs/coverage_env/bin/bowtie2
❯ bowtie2 --help
Bowtie 2 version 2.5.1 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]
...
❯ d_work="${HOME}/tsukiyamalab/Kris/2023_rDNA/results" # ., "${d_work}"
❯ if [[ ! -d "${d_work}/2023-0406" ]]; then
> mkdir -p "${d_work}/2023-0406/bams/err_out"
> fi
mkdir: created directory '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406'
mkdir: created directory '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams'
mkdir: created directory '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out'
❯ cd "${d_work}"
❯ pwd
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results
❯ ., "${d_genome}"
total 21M
drwxr-x--- 5 kalavatt 548 Apr 6 08:04 ./
drwxrwx--- 12 kalavatt 482 Apr 6 07:53 ../
drwxrwx--- 3 kalavatt 426 Apr 6 08:41 bowtie2/
drwxrwx--- 2 kalavatt 329 Mar 7 14:25 bwa/
drwxrwx--- 2 kalavatt 62 Mar 7 14:26 fasta/
-rw-r----- 1 kalavatt 3.6M Apr 27 2021 gene_association_R64-3-1_20210421.sgd.gz
-rw-r----- 1 kalavatt 1.1M Apr 21 2021 NotFeature_R64-3-1_20210421.fasta.gz
-rw-r----- 1 kalavatt 3.7M Apr 21 2021 orf_coding_all_R64-3-1_20210421.fasta.gz
-rw-r----- 1 kalavatt 2.6M Apr 21 2021 orf_trans_all_R64-3-1_20210421.fasta.gz
-rw-r----- 1 kalavatt 187K Apr 21 2021 other_features_genomic_R64-3-1_20210421.fasta.gz
-rw-r----- 1 kalavatt 42K Apr 27 2021 rna_coding_R64-3-1_20210421.fasta.gz
-rw-r----- 1 kalavatt 3.7M Apr 21 2021 S288C_reference_sequence_R64-3-1_20210421.fsa.gz
-rw-r----- 1 kalavatt 5.1M Apr 27 2021 saccharomyces_cerevisiae_R64-3-1_20210421.gff.gz
❯ ., "${f_genome}"
-rw-r----- 1 kalavatt 12M Apr 21 2021 /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
❯ ., "${f_indices}"*
-rw-rw---- 1 kalavatt 7.9M Apr 6 08:41 /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421.1.bt2
-rw-rw---- 1 kalavatt 2.9M Apr 6 08:41 /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421.2.bt2
-rw-rw---- 1 kalavatt 161 Apr 6 08:41 /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421.3.bt2
-rw-rw---- 1 kalavatt 2.9M Apr 6 08:41 /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421.4.bt2
-rw-rw---- 1 kalavatt 7.9M Apr 6 08:41 /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421.rev.1.bt2
-rw-rw---- 1 kalavatt 2.9M Apr 6 08:41 /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421.rev.2.bt2
❯ ., "${err_out}"
total 80K
drwxrws--- 2 kalavatt 0 Apr 6 08:58 ./
drwxrws--- 3 kalavatt 25 Apr 6 08:58 ../
❯ p_data="${HOME}/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed"
❯ unset fastqs
❯ typeset -a fastqs=(
> "${p_data}/Brn1_Q_rep1_ChIP.fastq"
> "${p_data}/Brn1_Q_rep1_input.fastq"
> "${p_data}/Brn1_Q_rep2_ChIP.fastq"
> "${p_data}/Brn1_Q_rep2_input.fastq"
> "${p_data}/Brn1_Q_rep3_ChIP.fastq"
> "${p_data}/Brn1_Q_rep3_input.fastq"
> "${p_data}/Brn1_Q_all_input.fastq"
> "${p_data}/Brn1_Q_all_ChIP.fastq"
> "${p_data}/Brn1_log_rep1_ChIP.fastq"
> "${p_data}/Brn1_log_rep1_input.fastq"
> "${p_data}/Brn1_log_rep2_ChIP.fastq"
> "${p_data}/Brn1_log_rep2_input.fastq"
> "${p_data}/Brn1_log_rep3_ChIP.fastq"
> "${p_data}/Brn1_log_rep3_input.fastq"
> "${p_data}/Brn1_log_all_ChIP.fastq"
> "${p_data}/Brn1_log_all_input.fastq"
> )
❯ for i in "${fastqs[@]}"; do ., "${i}"; done
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep1_ChIP.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175375.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep1_input.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175376.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep2_ChIP.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175377.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep2_input.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175378.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep3_ChIP.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175379.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep3_input.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175380.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_all_input.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175382.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_all_ChIP.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175381.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep1_ChIP.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175367.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep1_input.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175368.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep2_ChIP.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175369.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep2_input.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175370.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep3_ChIP.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175371.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep3_input.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175372.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_all_ChIP.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175373.fastq
lrwxrwxrwx 1 kalavatt 76 Apr 6 07:17 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_all_input.fastq -> /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/SRR7175374.fastq
❯ for i in "${fastqs[@]}"; do
> echo """
> bowtie2 \\
> -p ${threads} \\
> --very-sensitive-local \\
> -x ${f_indices} \\
> -U ${i} \\
> | samtools sort \\
> -@ ${threads} \\
> -l 0 \\
> -O bam \\
> | samtools view \\
> -@ ${threads} \\
> -O bam \\
> -o ${i%.fastq}.bam \\
> > >(tee -a ${err_out}/bowtie2_samtools-sort_samtools-view.stdout.txt) \\
> 2> >(tee -a ${err_out}/bowtie2_samtools-sort_samtools-view.stderr.txt)
> """
>
> # bowtie2 \
> # -p "${threads}" \
> # --very-sensitive-local \
> # -x "${f_indices}" \
> # -U "${i}" \
> # | samtools sort \
> # -@ "${threads}" \
> # -l 0 \
> # -O "bam" \
> # | samtools view \
> # -@ "${threads}" \
> # -O "bam" \
> # -o "${i%.fastq}.bam" \
> # > >(tee -a ${err_out}/bowtie2_samtools-sort_samtools-view.stdout.txt) \
> # 2> >(tee -a ${err_out}/bowtie2_samtools-sort_samtools-view.stderr.txt)
>
> if [[ -f "${i%.fastq}.bam" ]]; then
> samtools index \
> -@ "${threads}" \
> "${i%.fastq}.bam" \
> > >(tee -a ${err_out}/samtools-index.stdout.txt) \
> 2> >(tee -a ${err_out}/samtools-index.stderr.txt)
> fi
> done
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep1_ChIP.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep1_ChIP.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep1_input.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep1_input.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep2_ChIP.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep2_ChIP.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep2_input.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep2_input.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep3_ChIP.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep3_ChIP.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep3_input.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_rep3_input.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_all_input.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_all_input.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_all_ChIP.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_Q_all_ChIP.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep1_ChIP.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep1_ChIP.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep1_input.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep1_input.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep2_ChIP.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep2_ChIP.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep2_input.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep2_input.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep3_ChIP.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep3_ChIP.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep3_input.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_rep3_input.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_all_ChIP.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_all_ChIP.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
bowtie2 \
-p 16 \
--very-sensitive-local \
-x /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/bowtie2/S288C_reference_sequence_R64-3-1_20210421 \
-U /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_all_input.fastq \
| samtools sort \
-@ 16 \
-l 0 \
-O bam \
| samtools view \
-@ 16 \
-O bam \
-o /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/data/PRJNA471802/renamed/Brn1_log_all_input.bam \
> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stdout.txt) \
2> >(tee -a /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/err_out/bowtie2_samtools-sort_samtools-view.stderr.txt)
❯ for i in "${fastqs[@]}"; do
> # i="${fastqs[0]}" # echo "${i}"
>
> # echo """
> # bowtie2 \\
> # -p ${threads} \\
> # --very-sensitive-local \\
> # -x ${f_indices} \\
> # -U ${i} \\
> # | samtools sort \\
> # -@ ${threads} \\
> # -l 0 \\
> # -O bam \\
> # | samtools view \\
> # -@ ${threads} \\
> # -O bam \\
> # -o ${i%.fastq}.bam \\
> # > >(tee -a ${err_out}/bowtie2_samtools-sort_samtools-view.stdout.txt) \\
> # 2> >(tee -a ${err_out}/bowtie2_samtools-sort_samtools-view.stderr.txt)
> # """
>
> in_fastq="${i}" # ., "${in_fastq}"
> out_bam="${d_bams}/$(basename "${in_fastq}" .fastq).bam" # echo "${out_bam}"
> echo "#### $(basename ${in_fastq}) ####"
> {
> bowtie2 \
> -p "${threads}" \
> --very-sensitive-local \
> -x "${f_indices}" \
> -U "${in_fastq}" \
> | samtools sort \
> -@ "${threads}" \
> -l 0 \
> -O "bam" \
> | samtools view \
> -@ "${threads}" \
> -O "bam" \
> -o "${out_bam}"
> } \
> >> >(tee -a ${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort_samtools-view.stdout.txt) \
> 2>> >(tee -a ${err_out}/$(basename "${out_bam}" .bam).bowtie2_samtools-sort_samtools-view.stderr.txt)
>
> echo ""
> if [[ -f "${out_bam}" ]]; then
> samtools index \
> -@ "${threads}" \
> "${out_bam}" \
> > >(tee -a ${err_out}/$(basename "${out_bam}" .bam).samtools-index.stdout.txt) \
> 2> >(tee -a ${err_out}/$(basename "${out_bam}" .bam).samtools-index.stderr.txt)
> fi
> echo ""
> done
#### Brn1_Q_rep1_ChIP.fastq ####
7627718 reads; of these:
7627718 (100.00%) were unpaired; of these:
2074925 (27.20%) aligned 0 times
3727744 (48.87%) aligned exactly 1 time
1825049 (23.93%) aligned >1 times
72.80% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_Q_rep1_input.fastq ####
11331936 reads; of these:
11331936 (100.00%) were unpaired; of these:
504957 (4.46%) aligned 0 times
8094263 (71.43%) aligned exactly 1 time
2732716 (24.12%) aligned >1 times
95.54% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_Q_rep2_ChIP.fastq ####
6881074 reads; of these:
6881074 (100.00%) were unpaired; of these:
1342180 (19.51%) aligned 0 times
3424381 (49.77%) aligned exactly 1 time
2114513 (30.73%) aligned >1 times
80.49% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_Q_rep2_input.fastq ####
13059890 reads; of these:
13059890 (100.00%) were unpaired; of these:
544018 (4.17%) aligned 0 times
8941678 (68.47%) aligned exactly 1 time
3574194 (27.37%) aligned >1 times
95.83% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_Q_rep3_ChIP.fastq ####
9660608 reads; of these:
9660608 (100.00%) were unpaired; of these:
780964 (8.08%) aligned 0 times
5687748 (58.88%) aligned exactly 1 time
3191896 (33.04%) aligned >1 times
91.92% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_Q_rep3_input.fastq ####
11160513 reads; of these:
11160513 (100.00%) were unpaired; of these:
367228 (3.29%) aligned 0 times
8780918 (78.68%) aligned exactly 1 time
2012367 (18.03%) aligned >1 times
96.71% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_Q_all_input.fastq ####
35552339 reads; of these:
35552339 (100.00%) were unpaired; of these:
1416168 (3.98%) aligned 0 times
25816812 (72.62%) aligned exactly 1 time
8319359 (23.40%) aligned >1 times
96.02% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_Q_all_ChIP.fastq ####
24169400 reads; of these:
24169400 (100.00%) were unpaired; of these:
4198054 (17.37%) aligned 0 times
12839822 (53.12%) aligned exactly 1 time
7131524 (29.51%) aligned >1 times
82.63% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_log_rep1_ChIP.fastq ####
6643463 reads; of these:
6643463 (100.00%) were unpaired; of these:
635238 (9.56%) aligned 0 times
3058150 (46.03%) aligned exactly 1 time
2950075 (44.41%) aligned >1 times
90.44% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_log_rep1_input.fastq ####
15256990 reads; of these:
15256990 (100.00%) were unpaired; of these:
782379 (5.13%) aligned 0 times
11368165 (74.51%) aligned exactly 1 time
3106446 (20.36%) aligned >1 times
94.87% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_log_rep2_ChIP.fastq ####
32074691 reads; of these:
32074691 (100.00%) were unpaired; of these:
3436279 (10.71%) aligned 0 times
14504051 (45.22%) aligned exactly 1 time
14134361 (44.07%) aligned >1 times
89.29% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_log_rep2_input.fastq ####
12144595 reads; of these:
12144595 (100.00%) were unpaired; of these:
593652 (4.89%) aligned 0 times
8936412 (73.58%) aligned exactly 1 time
2614531 (21.53%) aligned >1 times
95.11% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_log_rep3_ChIP.fastq ####
8783472 reads; of these:
8783472 (100.00%) were unpaired; of these:
430229 (4.90%) aligned 0 times
5187717 (59.06%) aligned exactly 1 time
3165526 (36.04%) aligned >1 times
95.10% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_log_rep3_input.fastq ####
8922323 reads; of these:
8922323 (100.00%) were unpaired; of these:
307004 (3.44%) aligned 0 times
6865933 (76.95%) aligned exactly 1 time
1749386 (19.61%) aligned >1 times
96.56% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_log_all_ChIP.fastq ####
47501626 reads; of these:
47501626 (100.00%) were unpaired; of these:
4501732 (9.48%) aligned 0 times
22749937 (47.89%) aligned exactly 1 time
20249957 (42.63%) aligned >1 times
90.52% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...
#### Brn1_log_all_input.fastq ####
36323908 reads; of these:
36323908 (100.00%) were unpaired; of these:
1683052 (4.63%) aligned 0 times
27170475 (74.80%) aligned exactly 1 time
7470381 (20.57%) aligned >1 times
95.37% overall alignment rate
[bam_sort_core] merging from 0 files and 16 in-memory blocks...Code: Examine flags in bam outfiles
#!/bin/bash
# Still in coverage_env (need samtools)
calculate_run_time() {
what="""
calculate_run_time()
--------------------
Calculate run time for chunk of code
:param 1: start time in \$(date +%s) format
:param 2: end time in \$(date +%s) format
:param 3: message to be displayed when printing the run time <chr>
#TODO Check that params are not empty or inappropriate formats or strings
"""
run_time="$(echo "${2}" - "${1}" | bc -l)"
echo ""
echo "${3}"
printf 'Run time: %dh:%dm:%ds\n' \
$(( run_time/3600 )) \
$(( run_time%3600/60 )) \
$(( run_time%60 ))
echo ""
}
display_spinning_icon() {
what="""
display_spinning_icon()
-----------------------
Display \"spinning icon\" while a background process runs
:param 1: PID of the last program the shell ran in the background (int)
:param 2: message to be displayed next to the spinning icon (chr)
#TODO Checks...
"""
spin="/|\\–"
i=0
while kill -0 "${1}" 2> /dev/null; do
i=$(( (i + 1) % 4 ))
printf "\r${spin:$i:1} %s" "${2}"
sleep .15
done
}
list_tally_flags() {
what="""
list_tally_flags()
------------------
List and tally flags in a bam infile; function acts on a bam infile to
perform piped commands (samtools view, cut, sort, uniq -c, sort -nr) that
list and tally flags; function writes the results to a txt outfile, the
name of which is derived from the txt infile
:param 1: name of bam infile, including path (chr)
#TODO Checks...
"""
start="$(date +%s)"
samtools view "${1}" \
| cut -d$'\t' -f 2 \
| sort \
| uniq -c \
| sort -nr \
> "${1/.bam/.flags.txt}" &
display_spinning_icon $! \
"Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on $(basename "${1}")... "
end="$(date +%s)"
echo ""
calculate_run_time "${start}" "${end}" \
"List and tally flags in $(basename "${1}")."
}
p_data="${HOME}/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams"
unset bams
typeset -a bams=(
"${p_data}/Brn1_Q_rep1_ChIP.bam"
"${p_data}/Brn1_Q_rep1_input.bam"
"${p_data}/Brn1_Q_rep2_ChIP.bam"
"${p_data}/Brn1_Q_rep2_input.bam"
"${p_data}/Brn1_Q_rep3_ChIP.bam"
"${p_data}/Brn1_Q_rep3_input.bam"
"${p_data}/Brn1_Q_all_input.bam"
"${p_data}/Brn1_Q_all_ChIP.bam"
"${p_data}/Brn1_log_rep1_ChIP.bam"
"${p_data}/Brn1_log_rep1_input.bam"
"${p_data}/Brn1_log_rep2_ChIP.bam"
"${p_data}/Brn1_log_rep2_input.bam"
"${p_data}/Brn1_log_rep3_ChIP.bam"
"${p_data}/Brn1_log_rep3_input.bam"
"${p_data}/Brn1_log_all_ChIP.bam"
"${p_data}/Brn1_log_all_input.bam"
)
# for i in "${bams[@]}"; do echo "${i}"; done
# for i in "${bams[@]}"; do ., "${i}"; done
for i in "${bams[@]}"; do
# i="${bams[0]}" # echo "${i}"
echo "#### $(basename ${i}) ####"
list_tally_flags "${i}"
echo ""
done
for i in "${bams[@]}"; do
if [[ -f "${i/.bam/.flags.txt}" ]]; then
echo "#### $(basename ${i}) ####"
cat "${i/.bam/.flags.txt}"
echo ""
fi
done
samtools view Brn1_log_all_ChIP.bam | head
#NOTE Weird chromosome names; need to fix themPrinted: Examine flags in bam outfiles
❯ typeset -a bams=(
> "${p_data}/Brn1_Q_rep1_ChIP.bam"
> "${p_data}/Brn1_Q_rep1_input.bam"
> "${p_data}/Brn1_Q_rep2_ChIP.bam"
> "${p_data}/Brn1_Q_rep2_input.bam"
> "${p_data}/Brn1_Q_rep3_ChIP.bam"
> "${p_data}/Brn1_Q_rep3_input.bam"
> "${p_data}/Brn1_Q_all_input.bam"
> "${p_data}/Brn1_Q_all_ChIP.bam"
> "${p_data}/Brn1_log_rep1_ChIP.bam"
> "${p_data}/Brn1_log_rep1_input.bam"
> "${p_data}/Brn1_log_rep2_ChIP.bam"
> "${p_data}/Brn1_log_rep2_input.bam"
> "${p_data}/Brn1_log_rep3_ChIP.bam"
> "${p_data}/Brn1_log_rep3_input.bam"
> "${p_data}/Brn1_log_all_ChIP.bam"
> "${p_data}/Brn1_log_all_input.bam"
> )
❯ for i in "${bams}"; do echo "${i}"; done
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep1_ChIP.bam
❯ for i in "${bams[@]}"; do echo "${i}"; done
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep1_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep1_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep2_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep2_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep3_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep3_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_all_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_all_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep1_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep1_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep2_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep2_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep3_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep3_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_all_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_all_input.bam
❯ for i in "${bams[@]}"; do ., "${i}"; done
-rw-rw---- 1 kalavatt 175M Apr 6 09:40 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep1_ChIP.bam
-rw-rw---- 1 kalavatt 279M Apr 6 09:40 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep1_input.bam
-rw-rw---- 1 kalavatt 154M Apr 6 09:41 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep2_ChIP.bam
-rw-rw---- 1 kalavatt 318M Apr 6 09:42 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep2_input.bam
-rw-rw---- 1 kalavatt 226M Apr 6 09:43 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep3_ChIP.bam
-rw-rw---- 1 kalavatt 262M Apr 6 09:44 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep3_input.bam
-rw-rw---- 1 kalavatt 814M Apr 6 09:47 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_all_input.bam
-rw-rw---- 1 kalavatt 532M Apr 6 09:50 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_all_ChIP.bam
-rw-rw---- 1 kalavatt 137M Apr 6 09:50 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep1_ChIP.bam
-rw-rw---- 1 kalavatt 378M Apr 6 09:53 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep1_input.bam
-rw-rw---- 1 kalavatt 614M Apr 6 09:57 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep2_ChIP.bam
-rw-rw---- 1 kalavatt 303M Apr 6 09:58 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep2_input.bam
-rw-rw---- 1 kalavatt 192M Apr 6 09:59 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep3_ChIP.bam
-rw-rw---- 1 kalavatt 213M Apr 6 10:00 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep3_input.bam
-rw-rw---- 1 kalavatt 911M Apr 6 10:05 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_all_ChIP.bam
-rw-rw---- 1 kalavatt 848M Apr 6 10:10 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_all_input.bam
❯ for i in "${bams[@]}"; do
> # i="${bams[0]}" # echo "${i}"
> echo "#### $(basename ${i}) ####"
> list_tally_flags "${i}"
> echo ""
> done
#### Brn1_Q_rep1_ChIP.bam ####
[1] 757
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_rep1_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_rep1_ChIP.bam.
Run time: 0h:0m:7s
#### Brn1_Q_rep1_input.bam ####
[1] 818
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_rep1_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_rep1_input.bam.
Run time: 0h:0m:10s
#### Brn1_Q_rep2_ChIP.bam ####
[1] 904
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_rep2_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_rep2_ChIP.bam.
Run time: 0h:0m:6s
#### Brn1_Q_rep2_input.bam ####
[1] 959
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_rep2_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_rep2_input.bam.
Run time: 0h:0m:11s
#### Brn1_Q_rep3_ChIP.bam ####
[1] 1118
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_rep3_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_rep3_ChIP.bam.
Run time: 0h:0m:8s
#### Brn1_Q_rep3_input.bam ####
[1] 1219
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_rep3_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_rep3_input.bam.
Run time: 0h:0m:10s
#### Brn1_Q_all_input.bam ####
[1] 1298
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_all_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_all_input.bam.
Run time: 0h:0m:32s
#### Brn1_Q_all_ChIP.bam ####
[1] 1554
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_all_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_all_ChIP.bam.
Run time: 0h:0m:20s
#### Brn1_log_rep1_ChIP.bam ####
[1] 1709
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_rep1_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_rep1_ChIP.bam.
Run time: 0h:0m:6s
#### Brn1_log_rep1_input.bam ####
[1] 1760
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_rep1_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_rep1_input.bam.
Run time: 0h:0m:13s
#### Brn1_log_rep2_ChIP.bam ####
[1] 1858
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_rep2_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_rep2_ChIP.bam.
Run time: 0h:0m:27s
#### Brn1_log_rep2_input.bam ####
[1] 2055
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_rep2_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_rep2_input.bam.
Run time: 0h:0m:11s
#### Brn1_log_rep3_ChIP.bam ####
[1] 2202
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_rep3_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_rep3_ChIP.bam.
Run time: 0h:0m:8s
#### Brn1_log_rep3_input.bam ####
[1] 2270
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_rep3_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_rep3_input.bam.
Run time: 0h:0m:8s
#### Brn1_log_all_ChIP.bam ####
[1] 2335
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_all_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_all_ChIP.bam.
Run time: 0h:0m:41s
#### Brn1_log_all_input.bam ####
[1] 2644
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_all_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_all_input.bam.
Run time: 0h:0m:33s
#### Brn1_Q_rep1_ChIP.bam ####
2782361 0
2770432 16
2074925 4
#### Brn1_Q_rep1_input.bam ####
5416610 0
5410369 16
504957 4
#### Brn1_Q_rep2_ChIP.bam ####
2770893 0
2768001 16
1342180 4
#### Brn1_Q_rep2_input.bam ####
6262802 0
6253070 16
544018 4
#### Brn1_Q_rep3_ChIP.bam ####
4441272 16
4438372 0
780964 4
#### Brn1_Q_rep3_input.bam ####
5400653 0
5392632 16
367228 4
#### Brn1_Q_all_input.bam ####
17080375 0
17055796 16
1416168 4
#### Brn1_Q_all_ChIP.bam ####
9991973 0
9979373 16
4198054 4
#### Brn1_log_rep1_ChIP.bam ####
3014203 16
2994022 0
635238 4
#### Brn1_log_rep1_input.bam ####
7239390 0
7235221 16
782379 4
#### Brn1_log_rep2_ChIP.bam ####
14322187 0
14316225 16
3436279 4
#### Brn1_log_rep2_input.bam ####
5783228 0
5767715 16
593652 4
#### Brn1_log_rep3_ChIP.bam ####
4176724 0
4176519 16
430229 4
#### Brn1_log_rep3_input.bam ####
4309260 16
4306059 0
307004 4
#### Brn1_log_all_ChIP.bam ####
21506703 16
21493191 0
4501732 4
#### Brn1_log_all_input.bam ####
17328645 0
17312211 16
1683052 4
❯ samtools view Brn1_log_all_ChIP.bam | head
SRR7175373.380283 0 ref|NC_001133| 1 25 31M1I18M * 0 0 CCACACCACACCCACACACCCACACACCACACCCACACACCACACCACAC GGGGGIIIIIIIIIIIIIIIIIIIIIIIGIIIIIIIIIGGGGIGGGGGGI AS:i:90 XS:i:62 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:49 YT:Z:UU
SRR7175373.767277 0 ref|NC_001133| 1 14 1S31M1I17M * 0 0 CCCACACCACACCCACACACCCACACACCACACCCACACACCACACCACA AGGAAGGGGGG<GA.<GGGAAGGIGGGG....<GGGGGA.A.<AGGGGAA AS:i:88 XS:i:82 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:48 YT:Z:UU
SRR7175373.2091997 0 ref|NC_001133| 1 37 1S49M * 0 0 CCCACACCACACCCACACACCCACACACCACACCACACACCACACCACAC ...GA<AGAGGA<AAGGAGGGGA<AAAGGAGGIIGGAG<AGGIGAGGIGG AS:i:98 XS:i:67 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:49 YT:Z:UU
SRR7175373.2270050 0 ref|NC_001133| 1 11 9S41M * 0 0 ACACCACACCCACACCACACCCACACACCCACACACCACACCACACACCA GGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG AS:i:82 XS:i:78 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:41 YT:Z:UU
SRR7175373.7025590 0 ref|NC_001133| 1 14 8S42M * 0 0 CACCACACCCACACCACACCCACACACCCACACACCACACCACACACCAC GAGGAGG<<AG.<.<<<<G<<<GGGGGGGGGGGGGGGGAGGAGAAAAAG# AS:i:84 XS:i:78 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YT:Z:UU
SRR7175373.8104795 0 ref|NC_001133| 1 21 4S46M * 0 0 ACACCCACACCACACCCACACACCCACACACCACACCACACACCACACCA GGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:92 XS:i:68 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:46 YT:Z:UU
SRR7175373.8877369 0 ref|NC_001133| 1 1 4S31M1I14M * 0 0 ACACCCACACCACACCCACACACCCACACACCACACCCACACACCACACC AGA.AGGGGIAGAGGGGGGGGGGG.<.<GAGAGG.<.G<AAGGGG##### AS:i:82 XS:i:82 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:45 YT:Z:UU
SRR7175373.9602499 0 ref|NC_001133| 1 14 5S45M * 0 0 CACACCCACACCACACCCACACACCCACACACCACACCACACACCACACC GGAGAGGGIIIIGIIIIIIIIIIIIIIIIIIIIIIIIGIIIIIIIIIIII AS:i:90 XS:i:82 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:45 YT:Z:UU
SRR7175373.9864638 0 ref|NC_001133| 1 14 7S43M * 0 0 ACCACACCCACACCACACCCACACACCCACACACCACACCACACACCACA GGAAGIGIIIIIGGGIIIIIGIGGIIGGIIIGGGGIIIGIIGGGGIGIGG AS:i:86 XS:i:80 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:43 YT:Z:UU
SRR7175373.11488836 0 ref|NC_001133| 1 11 2S31M1I16M * 0 0 ACCCACACCACACCCACACACCCACACACCACACCCACACACCACACCAC AAAAGAAAGGGGAGGGGIIII.AAAAGGGGGGIG.GGGI<GG<.<AAAGA AS:i:86 XS:i:82 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:47 YT:Z:UUCode: Get jvarkit bamrenamechr up and running
#!/bin/bash
# Still in coverage_env
#+
#+ Use jvarkit from Pierre Lindenbaum: github.com/lindenb/jvarkit
#+ Pre-compiled jar here: uncloud.univ-nantes.fr/index.php/s/4sL77oWR2BFzSBH
#+
#+ In particular, jvarkit utility bamrenamechr
#NOTE Below chunk is not necessary
# module load picard/2.25.1-Java-11
#
# f_genome="${d_genome}/fasta/S288C_reference_sequence_R64-3-1_20210421.fa" # ., "${f_genome}"
# f_dict="${f_genome/.fa/.dict}"
# java -jar "${EBROOTPICARD}/picard.jar" CreateSequenceDictionary \
# --REFERENCE "${f_genome}" \
# --OUTPUT "${f_dict}"
#
# ., "${f_dict}"
# cat "${f_dict}"
#
# module purge
module load Java/1.8.0_181
f_jar="${HOME}/tsukiyamalab/Kris/2023_rDNA/software/jvarkit/jvarkit.jar" # ., ${f_jar}
java -jar "${f_jar}" bamrenamechr --help
pwd
if [[ ! -f test-jvarkit.bam ]]; then
cp Brn1_log_rep1_ChIP.bam test-jvarkit.bam
samtools index -@ "${SLURM_CPUS_ON_NODE}" test-jvarkit.bam
# samtools idxstats test-jvarkit.bam \
# | grep -v -F '*' \
# | awk '{printf("%s\tchr%s\n",$1,$1);}' \
# > test-jvarkit.txt
fi
# Create a custom dictionary (tab-separated) mapping current chromosome names
#+ to desired chromosome names
cat test-jvarkit.txt
java -jar "${f_jar}" bamrenamechr --help
java -jar "${f_jar}" bamrenamechr \
-f test-jvarkit.txt \
test-jvarkit.bam \
> test-jvarkit.renamed.bam
samtools view test-jvarkit.renamed.bam | head # Looks good
samtools view test-jvarkit.renamed.bam | tail # Looks good
if [[ -f test-jvarkit.renamed.bam ]]; then
cp test-jvarkit.txt dictionary_chr-names.txt
rm test-jvarkit.*
fiPrinted: Get jvarkit bamrenamechr up and running
❯ module load picard/2.25.1-Java-11
To execute picard run: java -jar $EBROOTPICARD/picard.jar
❯ f_dict="${f_genome/.fa/.dict}"
❯ java -jar "${EBROOTPICARD}/picard.jar" CreateSequenceDictionary \
> --REFERENCE "${f_genome}" \
> --OUTPUT "${f_dict}"
11:30:23.947 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/app/software/picard/2.25.1-Java-11/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Thu Apr 06 11:30:23 PDT 2023] CreateSequenceDictionary --OUTPUT /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.dict --REFERENCE /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 06 11:30:23 PDT 2023] Executing as kalavatt@gizmoj10 on Linux 4.15.0-192-generic amd64; OpenJDK 64-Bit Server VM 11.0.2+9; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: Version:2.25.1
[Thu Apr 06 11:30:24 PDT 2023] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2147483648
❯ ., "${f_dict}"
-rw-rw---- 1 kalavatt 3.5K Apr 6 11:30 /home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.dict
❯ cat "${f_dict}"
@HD VN:1.6
@SQ SN:ref|NC_001133| LN:230218 M5:6681ac2f62509cfc220d78751b8dc524 UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001134| LN:813184 M5:97a317c689cbdd7e92a5c159acd290d2 UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001135| LN:316620 M5:54f4a74aa6392d9e19b82c38aa8ab345 UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001136| LN:1531933 M5:74180788027e20df3de53dcb2367d9e3 UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001137| LN:576874 M5:d2787193198c8d260f58f2097f9e1e39 UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001138| LN:270161 M5:b7ebc601f9a7df2e1ec5863deeae88a3 UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001139| LN:1090940 M5:a308c7ebf0b67c4926bc190dc4ba8ed8 UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001140| LN:562643 M5:f66a4f8eef89fc3c3a393fe0210169f1 UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001141| LN:439888 M5:4eae53ae7b2029b7e1075461c3eb9aac UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001142| LN:745751 M5:6757b8c7d9cca2c56401e2484cf5e2fb UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001143| LN:666816 M5:e72df2471be793f8aa06850348a896fa UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001144| LN:1078177 M5:77945d734ab92ad527d8920c9d78ac1c UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001145| LN:924431 M5:073f9ff1c599c1a6867de2c7e4355394 UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001146| LN:784333 M5:188bca5110182a786cd42686ec6882c6 UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001147| LN:1091291 M5:7e02090a38f05459102d1a9a83703534 UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001148| LN:948066 M5:232475e9a61a5e07f9cb2df4a2dad757 UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
@SQ SN:ref|NC_001224| LN:85779 M5:71c39cf065b8d574f636b654c274cf1b UR:file:/home/kalavatt/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/fasta/S288C_reference_sequence_R64-3-1_20210421.fa
❯ module purge
❯ module load Java/1.8.0_181
❯ java -jar "${f_jar}" bamrenamechr --help
Usage: bamrenamechr [options] Files
Options:
--bamcompression
Compression Level. 0: no compression. 9: max compression;
Default: 5
--dict
Use this new dictionary A SAM Sequence dictionary source: it can be a
*.dict file, a fasta file indexed with 'picard
CreateSequenceDictionary', or any hts file containing a dictionary (VCF,
BAM, CRAM, intervals...)
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-i, --ignore
If the tool cannot convert a contig, skip the read
Default: false
-f, --mapping, -m
load a custom name mapping. Format (chrom-source\tchrom-dest\n)+
-o, --out
Output file. Optional . Default: stdout
-R, --reference
For Reading CRAM. Indexed fasta Reference file. This file must be
indexed with samtools faidx and with picard CreateSequenceDictionary
--samoutputformat
Sam output format.
Default: SAM
Possible Values: [BAM, SAM, CRAM]
--version
print version and exit
❯ pwd
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams
❯ if [[ ! -f test-jvarkit.bam ]]; then
> cp Brn1_log_rep1_ChIP.bam test-jvarkit.bam
> samtools index -@ ${SLURM_CPUS_ON_NODE} test-jvarkit.bam
> samtools idxstats test-jvarkit.bam \
> | grep -v -F '*' \
> | awk '{printf("%s\tchr%s\n",$1,$1);}' \
> > test-jvarkit.txt
> fi
'Brn1_log_rep1_ChIP.bam' -> 'test-jvarkit.bam'
❯ # Create a custom dictionary mapping current chromosome names to desired
❯ #+ chromosome names
❯ cat test-jvarkit.txt
ref|NC_001133| I
ref|NC_001134| II
ref|NC_001135| III
ref|NC_001136| IV
ref|NC_001137| V
ref|NC_001138| VI
ref|NC_001139| VII
ref|NC_001140| VIII
ref|NC_001141| IX
ref|NC_001142| X
ref|NC_001143| XI
ref|NC_001144| XII
ref|NC_001145| XIII
ref|NC_001146| XIV
ref|NC_001147| XV
ref|NC_001148| XVI
ref|NC_001224| Mito
❯ java -jar "${f_jar}" bamrenamechr \
> -f test-jvarkit.txt \
> test-jvarkit.bam \
> > test-jvarkit.renamed.bam
[WARN][ConvertBamChromosomes]num ignored read:0
❯ zcat ~/tsukiyamalab/Kris/genomes/S288C_reference_genome_R64-3-1_20210421/S288C_reference_sequence_R64-3-1_20210421.fsa.gz | grep "^>"
>ref|NC_001133| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=I]
>ref|NC_001134| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=II]
>ref|NC_001135| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=III]
>ref|NC_001136| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=IV]
>ref|NC_001137| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=V]
>ref|NC_001138| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=VI]
>ref|NC_001139| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=VII]
>ref|NC_001140| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=VIII]
>ref|NC_001141| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=IX]
>ref|NC_001142| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=X]
>ref|NC_001143| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XI]
>ref|NC_001144| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XII]
>ref|NC_001145| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XIII]
>ref|NC_001146| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XIV]
>ref|NC_001147| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XV]
>ref|NC_001148| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XVI]
>ref|NC_001224| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [location=mitochondrion] [top=circular]Code: Run jvarkit bamrenamechr on problem bams
#!/bin/bash
# Still in coverage_env, and still have module Java/1.8.0_181 loaded
f_jar="${HOME}/tsukiyamalab/Kris/2023_rDNA/software/jvarkit/jvarkit.jar" # ., ${f_jar}
p_data="${HOME}/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams"
unset bams
typeset -a bams=(
"${p_data}/Brn1_Q_rep1_ChIP.bam"
"${p_data}/Brn1_Q_rep1_input.bam"
"${p_data}/Brn1_Q_rep2_ChIP.bam"
"${p_data}/Brn1_Q_rep2_input.bam"
"${p_data}/Brn1_Q_rep3_ChIP.bam"
"${p_data}/Brn1_Q_rep3_input.bam"
"${p_data}/Brn1_Q_all_input.bam"
"${p_data}/Brn1_Q_all_ChIP.bam"
"${p_data}/Brn1_log_rep1_ChIP.bam"
"${p_data}/Brn1_log_rep1_input.bam"
"${p_data}/Brn1_log_rep2_ChIP.bam"
"${p_data}/Brn1_log_rep2_input.bam"
"${p_data}/Brn1_log_rep3_ChIP.bam"
"${p_data}/Brn1_log_rep3_input.bam"
"${p_data}/Brn1_log_all_ChIP.bam"
"${p_data}/Brn1_log_all_input.bam"
)
# for i in "${bams[@]}"; do echo "${i}"; done
# for i in "${bams[@]}"; do ., "${i}"; done
for i in "${bams[@]}"; do
java -jar "${f_jar}" bamrenamechr \
-f dictionary_chr-names.txt \
"${i}" \
> "${i%.bam}.renamed.bam"
if [[ -f "${i%.bam}.renamed.bam" ]]; then
if [[ -s "${i%.bam}.renamed.bam" ]]; then
mv -f "${i%.bam}.renamed.bam" "${i}"
fi
fi
done
#NOTE 1/4 Did not set '--samoutputformat bam' when calling bamrenamechr, so the
#NOTE 2/4 outfiles are actually sams; thus, they need to have their extensions
#NOTE 3/4 changed, then I need to converted them to bams; finally, I need to
#NOTE 4/4 index the files
rm *.bai
rename 's/.bam/.sam/g' *.bam
for i in "${bams[@]}"; do
samtools view -@ "${SLURM_CPUS_ON_NODE}" -S -b "${i/.bam/.sam}" > "${i}"
doneCode: Run jvarkit bamrenamechr on problem bams
❯ for i in "${bams[@]}"; do
> java -jar "${f_jar}" bamrenamechr \
> -f dictionary_chr-names.txt \
> "${i}" \
> > "${i%.bam}.renamed.bam"
>
> if [[ -f "${i%.bam}.renamed.bam" ]]; then
> if [[ -s "${i%.bam}.renamed.bam" ]]; then
> mv -f "${i%.bam}.renamed.bam" "${i}"
> fi
> fi
> done
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep1_ChIP.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep1_ChIP.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep1_input.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep1_input.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep2_ChIP.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep2_ChIP.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep2_input.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep2_input.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep3_ChIP.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep3_ChIP.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep3_input.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_rep3_input.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_all_input.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_all_input.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_all_ChIP.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_Q_all_ChIP.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep1_ChIP.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep1_ChIP.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep1_input.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep1_input.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep2_ChIP.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep2_ChIP.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep2_input.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep2_input.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep3_ChIP.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep3_ChIP.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep3_input.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_rep3_input.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_all_ChIP.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_all_ChIP.bam'
[WARN][ConvertBamChromosomes]num ignored read:0
renamed '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_all_input.renamed.bam' -> '/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406/bams/Brn1_log_all_input.bam'
❯ rm *.baiCode: S288C_reference_sequence_R64-3-1_20210421.fa
#!/bin/bash
cd "${HOME}/genomes/S288C_reference_genome_R64-3-1_20210421/fasta"
cat S288C_reference_sequence_R64-3-1_20210421.fa \
sed
cp \
S288C_reference_sequence_R64-3-1_20210421.fa \
S288C_reference_sequence_R64-3-1_20210421.initial.fa
cat S288C_reference_sequence_R64-3-1_20210421.initial.fa \
| sed "s:.*NC_001133.*:>I:g" \
| sed "s:.*NC_001134.*:>II:g" \
| sed "s:.*NC_001135.*:>III:g" \
| sed "s:.*NC_001136.*:>IV:g" \
| sed "s:.*NC_001137.*:>V:g" \
| sed "s:.*NC_001138.*:>VI:g" \
| sed "s:.*NC_001139.*:>VII:g" \
| sed "s:.*NC_001140.*:>VIII:g" \
| sed "s:.*NC_001141.*:>IX:g" \
| sed "s:.*NC_001142.*:>X:g" \
| sed "s:.*NC_001143.*:>XI:g" \
| sed "s:.*NC_001144.*:>XII:g" \
| sed "s:.*NC_001145.*:>XIII:g" \
| sed "s:.*NC_001146.*:>XIV:g" \
| sed "s:.*NC_001147.*:>XV:g" \
| sed "s:.*NC_001148.*:>XVI:g" \
| sed "s:.*NC_001224.*:>Mito:g" \
> tmp
grep "^>" S288C_reference_sequence_R64-3-1_20210421.initial.fa
grep "^>" tmp
mv -f tmp S288C_reference_sequence_R64-3-1_20210421.faPrinted: S288C_reference_sequence_R64-3-1_20210421.fa
❯ cp \
> S288C_reference_sequence_R64-3-1_20210421.fa \
> S288C_reference_sequence_R64-3-1_20210421.initial.fa
'S288C_reference_sequence_R64-3-1_20210421.fa' -> 'S288C_reference_sequence_R64-3-1_20210421.initial.fa'
❯ grep "^>" S288C_reference_sequence_R64-3-1_20210421.initial.fa
>ref|NC_001133| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=I]
>ref|NC_001134| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=II]
>ref|NC_001135| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=III]
>ref|NC_001136| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=IV]
>ref|NC_001137| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=V]
>ref|NC_001138| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=VI]
>ref|NC_001139| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=VII]
>ref|NC_001140| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=VIII]
>ref|NC_001141| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=IX]
>ref|NC_001142| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=X]
>ref|NC_001143| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XI]
>ref|NC_001144| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XII]
>ref|NC_001145| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XIII]
>ref|NC_001146| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XIV]
>ref|NC_001147| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XV]
>ref|NC_001148| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [chromosome=XVI]
>ref|NC_001224| [org=Saccharomyces cerevisiae] [strain=S288C] [moltype=genomic] [location=mitochondrion] [top=circular]
❯ grep "^>" tmp
>I
>II
>III
>IV
>V
>VI
>VII
>VIII
>IX
>X
>XI
>XII
>XIII
>XIV
>XV
>XVI
>Mito
❯ mv -f tmp S288C_reference_sequence_R64-3-1_20210421.fa
renamed 'tmp' -> 'S288C_reference_sequence_R64-3-1_20210421.fa'
❯ for i in "${bams[@]}"; do
> samtools view -@ "${SLURM_CPUS_ON_NODE}" -S -b "${i/.bam/.sam}" > "${i}"
> doneCode:
#!/bin/bash
threads="${SLURM_CPUS_ON_NODE}"
input="${p_data}/Brn1_Q_rep1_input.bam"
IP="${p_data}/Brn1_Q_rep1_ChIP.bam"
samtools index -@ "${threads}" "${IP}"
samtools index -@ "${threads}" "${input}"
bamCompare \
-b1 "${IP}" \
-b2 "${input}" \
-o "${IP%%.IP.sort.bam}.input-normalized.bw" \
--binSize 10 \
--scaleFactorsMethod None \
--normalizeUsing BPM \
--numberOfProcessors "${threads}" \
> >(tee -a "${IP%%.IP.sort.bam}.stdout.txt") \
2> >(tee -a "${IP%%.IP.sort.bam}.stderr.txt")