m6Ad-SNVs

A Python pipeline for the analysis of variant-dependent m6A modifications within the Human genome.

Requirements

This pipeline requires Python 3.8 with the following packages:

• biopython (>=1.83)
• pandas (>=2.2.1)
• pysam (>=0.22.0)
• tqdm (>=4.38.0)
• wget (>=3.2)

They can be installed all at once by running pip over the requirements file under the src folder as follow:

pip install src/requirements.txt

It also requires RNAFold as an external software dependency as part of the ViennaRNA package. It can be easily installed with conda by typing the following command in your terminal:

conda install viennarna

Note: you need to add the bioconda channel to your conda instance before running installing the viennarna package. If you are wondering how to add the bioconda channel, have a look at the Bioconda website.

Usage

Once all the requirements are installed, you can finally run the pipeline which is all enclosed into the m6Ad-SNVs.py Python script. Here is a list of available options:

Option	Default	Mandatory	Description
--bed		⚑	Path to the BED file with the coordinates of the genomic regions of interest
--bed-skip-lines	0		Skip the first number of lines in the input BED file
--vcf		⚑	Path to the VCF file with the SNPs coordinates
--genome		⚑	Path to the fasta genome file
--search	[AGT][AG]AC[ACT]		Search for a specific pattern in the sequences. It accepts regular expressions. It searches for DRACH sites by default
--out-table			Path to the output file (optional, it overwrites the output file if it exists)
--out-html			Path to the output folder with RNAfold structures (optional, it overwrites the output files if they exist)
--nproc	1		Make it parallel
--version			Print the tool version and exit

Credits

Please credit our work in your manuscript by citing:

Manuscript in preparation

Support

If you need support, please open an Issue.