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Title: ncRNAScan: A pipeline to identify putative novel ncRNAs from deep sequencing data

Type Software BioCoder (2014): ncRNAScan: A pipeline to identify putative novel ncRNAs from deep sequencing data. Zenodo. Software. https://zenodo.org/record/11139

Author: BioCoder ;

Links

Summary

 

ncRNAScan is a pipeline to extract putative novel ncRNAs ab initio, given a list of transcripts in GTF format assembled from deep sequencing data (ex: RNA-Seq) and annotation data.

This pipeline script will bind together the functionality of the tools / scripts: cuffcompare, categorize_ncRNAs.pl, get_unique_features.pl, fetch_seq_from_ucsc.pl, RNAfold, Infernal and Coding Potential Calculator (CPC.sh). Transcriptome construction tools such as Cufflinks produces a set of assembled transcripts in GTF format. ncRNAScan uses this data in addition to known gene annotation to extract putative ncRNAs constructed by the ab initio assemblers. The pipeline relies on the FPKM / RPKM values generated by these assemblers to assess the confidence of the constructed de novo transcripts and validates it against the known refenrece gene and non coding RNA information to identify putative novel ncRNAs.

IO::Routine

The scripts use custom IO::Routine Perl Module.

If you are installing ncRNAScan Pipeline, IO::Routine module is automatically installed.

☲☴ ncRNAScan

Head on to NGS-Utils directory for script list.

Install ncRNAScan and all its dependencies (Mac and Linux):

cd /to/your/preferred/install/path curl -O https://raw.githubusercontent.com/biocoder/Perl-for-Bioinformatics/master/NGS-Utils/ncRNAScan perl ncRNAScan -setup

Documentation:

perl ncRNAScan -h

or

perldoc ncRNAScan

or to get help documentation for individual modules, do:

perl ncRNAScan -h cuff perl ncRNAScan -h cat perl ncRNAScan -h get perl ncRNAScan -h fetch perl ncRNAScan -h cpc perl ncRNAScan -h rna perl ncRNAScan -h inf

Known issues:

If pipeline setup fails due to XML::Parser module, you need to install XML parser C libraries.

On Ubuntu / Debian based Linux distributions, as root user, do:

apt-get install libexpat1 libexpat1-dev

On RedHat / Fedora / CentOS based Linux distributions, as root user do:

yum install expat expat-devel RNAfold: RNAfold is slow and does not work for sequences over 10000bp in length. I am working on including an alternative secondary structure prediction program instead of RNAfold. Meanwhile you may skip running RNAfold module by not issuing the --rnafold option with ncRNAScan.

Caveats:

The pipeline script uses a lot of inherent Linux core utils and has been only tested in BASH shell.

Citation

Konganti, Kranti (2014). ncRNAScan: A pipeline to identify putative novel ncRNAs from deep sequencing data. ZENODO. 10.5281/zenodo.10566

Cheers,

BioCoder

More information

  • DOI: 10.5281/zenodo.11139

Subjects

  • ncRNAScan, NGS, ncRNA, non-coding rna, lncrna, lincrna, ncrna prediction, ncrna rna-seq

Dates

  • Publication date: 2014
  • Issued: August 04, 2014

Rights

Much of the data past this point we don't have good examples of yet. Please share in #rdi slack if you have good examples for anything that appears below. Thanks!

Format

electronic resource

Relateditems

DescriptionItem typeRelationshipUri
IsSupplementTohttps://github.com/biocoder/Perl-for-Bioinformatics/tree/1.5
IsVersionOfhttps://doi.org/10.5281/zenodo.591764
IsPartOfhttps://zenodo.org/communities/zenodo