RNAmod

Find RNA modifications in sam files.

Requirements

• python >= 3
• node >= 8

Install

If you want only TSV (not graphic output) you can skip 2-4 steps.

1. Clone the repository

2. Make sure that your version of nodejs is higher than 8

sudo apt install nodejs
node --version

3. Install npmjs

sudo apt install npm
npm --version

4. Install puppeteer

npm install puppeteer

5. Install python dependencies

pip3 install -r requirements.txt

Usage

bin/rnamod OPTIONS
bin/rnamod --help

Miminal configurations

bin/rnamod --experiment exp1.sam exp2.sam \
           --checks chck1.sam chck.sam \
           --fasta seq1.fa seq2.fa seq3.fa \

Required options

--sam EXPERIMENT CHECK

• EXPERIMENT: Your experiment
• CHECK: Files wich will be compared to experiments

--fasta

• Sequence files
• Only FASTA format allowed

Optional options

--pattern

• Find pattern(s) in sequence
• [atcg]: pattern but unimportant bases
• [ATCG]: important bases (marked in outputs)
• [.]: any unimportant bases

--min-coverage

• Min coverage for each position

--max-pvalue

• Max pvalue when position is still significant

--min-stops-relative

• Min reltive stops when position is significant

--min-errors-relative

• Min relative erros when position is significant

--significant-stops-relative

• When stop is significant

--significant-errors-relative

• When error is significant

--significant-insertion-relative

• Significant insertion

--significant-deletion-relative

• Significant deletion

--max-pattern-missmatch

• Maximum missmatch allowed in pattern matching

--boundary

• Set boundaries for sequences (SEQUENCE FROM TO)
• For example if you want sequence HIVNL43 stop at position 9711
• --boundary HIVNL43 0 9711

--no-graphic

• No graphic output
• Useful if you don't have node installed

--no-tsv

• If you don't want TSV output

--outputs

• Custom directory where results are saved

Credits

• Ondřej Moravčík (@ondra-m)
• Jan Pačes (@hpaces)

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