IndelSearcher_CRISPR_CAS9

This version is not maintained now, move to https://github.com/CRISPRJWCHOI/CRISPR_toolkit

Prerequisite

OS Requirements: Linux(Ubuntu 16.04)
Install time: about 30 minutes

- python2.7
pip install numpy==1.12.1 pandas==0.20.1
or
- anaconda python2.7
conda install numpy=1.12.1 pandas=0.20.1

EMBOSS:6.6.0.0, needle
http://emboss.sourceforge.net/download/

Usage

./Project_list.txt
Write the one project name per line

/Input/FASTQ/<project_name>/<sample_name>.fastq
/Input/Reference/<project_name>/barcode.txt
/Input/Reference/<project_name>/Reference_sequence.txt
/Input/Reference/<project_name>/Target_region.txt

Test
python2.7 Run_indel_searcher_ver3.0.py --pam_type Cas9 --pam_pos Forward

Detailed options
python2.7 Run_indel_searcher_ver3.0.py -h

Output
/Output/<project_name>/Summary_result/Final_indel_result_<project_name>.tsv
Barcode            Total_indel  Total IND/TOT  Match    Info
CACCGACACACACACAGCAC    20      105     0.19    20.0    66M1I:12:60.0, 67M2D:8:40.0

/Output/<project_name>/Summary_result/Summary_result.tsv
Barcode                Total  Insertion Deletion Complex Total_indel IND/TOT
CACCGACACACACACAGCAC    105      12        8        0        20      0.190476190476

Random sequence generator

Prerequisite

- python2.7
pip install numpy==1.13
or
- anaconda python2.7
conda install numpy=1.13

Usage

python2.7 Random_sequence_generator.py 1000 23 0.2 0.3 0.2 0.3 random_seq.txt