https://github.com/Biobix/RiboZINB

RiboZinB: A tool to identifying actively translated isoform(s) from ribosome profiling data.
https://github.com/Biobix/RiboZINB

Last synced: 2 months ago
JSON representation

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

• Host: GitHub
• URL: https://github.com/Biobix/RiboZINB
• Owner: Biobix
• License: other
• Created: 2017-09-22T15:28:40.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2018-02-08T18:45:19.000Z (over 6 years ago)
• Last Synced: 2024-06-30T15:46:11.591Z (3 months ago)
• Language: Perl
• Homepage:
• Size: 1.28 MB
• Stars: 0
• Watchers: 5
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: License.txt

Awesome Lists containing this project

• awesome-riboseq - Code

README

        
# 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: [email protected] or [email protected]