PFv2: annotation-free computational method to identify post-transcriptional exon shuffling (PTES) events

LINKS:

PTESTinder: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-0881-4
PTESFinder v1: https://sourceforge.net/projects/ptesfinder-v1/files/

CHANGES:

Dependency on bowtie1 in the identification phase has been removed
Identification of putative backsplice events using STAR
Annotation-free backsplice identification

USAGE:

Input Files:
    RNASeq data in Illumina FASTQ format
    Genome reference in FASTA format
    Pre-built bowtie2 genome reference index
    Pre-built bowtie2 transcriptome reference index
    Path to pre-built STAR genome reference index files

Running PTESFinder:
        $ sh PFv2.sh <options>

Parameters:

Mandatory:
        -r sequence reads in FASTQ format
        -d working directory
        -i sample_id
        -t transcript reference bowtie index
        -g genome reference in FASTA format
        -b genome reference bowtie2 index
        -c PFv2 code directory
        -l average read length
        -S path to STAR genome reference index files
Optional:
        -p PID -- should be between 0 and 1; ideal values 0.60 - 0.95, default: 0.85
        -j junction Span --should be an even integer, ideal values between 4 and 14, default: 8
        -C Maximum backsplice genomic span - default: 1000000

DEPENDENCIES:

Python 3 - including argparse, subprocess, os, logging
Java > 15
STAR: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Memory requirements are genome size and aligner dependent - see STAR aligner information for details