RiboZinB: A tool to identifying actively translated isoform(s) from ribosome profiling data.
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RiboZINB.pl

README.md

RiboZINB

RiboZinB: A tool to identifying actively translated isoform(s) from ribosome profiling data. The case of the Zero-inflated model.

The software was created at VIB-UGent Center for Medical Biotechnology and Lab of Bioinformatics and Computational Genomics (Biobix), University of Gent, belgium.

Requirements

The RiboZINB software is primarily written in perl and R.

Perl packages:
--------------
	- Perl + v.5.10+
	- Getopt::Long
	- Cwd	
	- BioPerl
	- POSIX
	- Parallel::ForkManager
	- File::Spec
	
R packages:
--------------
	- ggplot2
	- pscl
	- VGAM

Install

RiboZINB does not rerquire any special installation requirements. To install RiboZINB, clone/download the github repository into a directory of your choice.

USAGE: perl ./RiboZINB.pl -p positional_data_file -g gtf_file -s script_dir -r total_mappable_reads

Mandatory input parameters
-p RIBO-seq positional data in comma delimited format [chromosome,strand,start,count]
-g annoation in gtf format
-s script directory
-r total number of mappable reads

Optional input parameters
-e experiment name
-w work directory
-m minimum reads count
-d delete work directory if it exist
-t number of processors to use
-n number of iterations when generating negative set
-f FDR threshold
-v Default RPSS threshold [v=0.1]
-dt flag to determine if we use default RPSS threshold [0.1] or estimate threshold by permutation test.
-a multiplier to adjust for noise

Output files
*_gene_list.txt this file contains the list of all protein coding genes evaluated in the analysis
*_all_transcript.txt File consisting of all protein coding transcripts from the genes in *_gene_list.txt
*_transcript_zeroinfl.txt file consisting of transcripts from _all_transcript.txt that pass the S-curve thresholds alongside their RiboZinB scores and P-values
*_Ribo_expressed_isoform.txt consist of the list of transcripts/isoforms predicted by the RiboZinB algorithm i.e. transcripts that fall below the FDR threshold
*_Ribo_distribution.pdf plot of the empirical and observed distributions of the RPSS scores
*_scurve.pdf plot of the fitted s-curve model overlay of on the longest CCDS (canonical isoform) and the log RPKM and CDS coverage thresholds

More information

For more information about RiboZINB contact: elvis.ndah@gmail.com or Gerben.Menschaert@UGent.be