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

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). 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 informationto 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

• Caveats:

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

Cheers,

BioCoder