Massively parallel reporter assay (MPRA) data analysis pipeline

This repository contains scripts used to analyse MPRA sequencing data

Requirements

• python >3.0
• Biopython
• samtools
• Burrows-Wheeler Aligner (BWA)
• cutadapt
• seqtk

Usage

python mpra_pipeline.py -h

usage: mpra_pipeline.py [-h] [-r1 READ1] [-r2 READ2] [-ds1 DNA_SEQ1 [DNA_SEQ1 ...]] [-ds2 DNA_SEQ2 [DNA_SEQ2 ...]] -o OUTDIR [-i INDEX_DIR] -m {enhancer,cdna,gdna}

MPRA sequencing data analysis pipeline.

optional arguments:
-h, --help            show this help message and exit
-r1 READ1, --read1 READ1
                      Path to a gzipped fastq file. Sequences in this file will be mapped against the reference MPRA library to find refSNP containing reads. Required if run --mode='enhancer'.
-r2 READ2, --read2 READ2
                      Path to a gzipped fastq file. Sequences in this file will be used to search for barcodes of refSNPs. Required if run --mode='enhancer'.
-ds1 DNA_SEQ1 [DNA_SEQ1 ...], --dna-seq1 DNA_SEQ1 [DNA_SEQ1 ...]
                      Provide a fastq file or a list of space separated fastq files (forward reads) containing 1) cDNA sequences (required if run --mode='cdna') 2) gDNA sequences (required if run
                      --mode='gdna').
-ds2 DNA_SEQ2 [DNA_SEQ2 ...], --dna-seq2 DNA_SEQ2 [DNA_SEQ2 ...]
                      Provide a fastq file or a list of space separated fastq files (reverse reads) containing 1) cDNA sequences (required if run --mode='cdna') or 2) gDNA sequences (required if run
                      --mode='gdna').
-o OUTDIR, --outdir OUTDIR
                      Provide a path to save output files.
-i INDEX_DIR, --index-dir INDEX_DIR
                      Provide path to the directory where reference index (generated using bwa) files are located and also include prefix of the file
-m {enhancer,cdna,gdna}, --mode {enhancer,cdna,gdna}
                      Choose a run mode to find the barcodes from enhancer, cDNA or gDNA sequences