biocoder / perl-for-bioinformatics

An attempt to help anyone interested in using Perl for Bioinformatics

Bioinformatics tools written in Perl

Most of the scripts here were written while I was working on different projects, which I think will be useful to others and can be extended / modified per there needs.

IO::Routine

• The scripts use custom IO::Routine Perl Module.

• Please see the installation instructions by browsing the IO::Routine directory.

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

• Requires Bio::SeqIO module be installed and available.

☲☴ lncRNApipe

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

• Head on to NGS-Utils directory for script list.

• Install lncRNApipe and all its dependencies (Mac and Linux):

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

• Documentation:

      perl lncRNApipe --h
  

or

      perldoc lncRNApipe

or to get help documentation for individual modules, do:

  	  perl lncRNApipe --h cuff
  	  perl lncRNApipe --h cat
  	  perl lncRNApipe --h get
  	  perl lncRNApipe --h fetch
  	  perl lncRNApipe --h cpc
  	  perl lncRNApipe --h rna
  	  perl lncRNApipe --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.
  • Please use absolute full PATH names. Instead of using lncRNApipe --run ./lncRNApipe_output ..., use lncRNApipe --run /data/lncRNApipe_output ...

Cite lncRNApipe:

Assessment of Histone Tail Modifications and Transcriptional Profiling During Colon Cancer Progression Reveals a Global Decrease in H3K4me3 Activity Karen Triff; Mathew W McLean; Kranti Kranti; Jiahui Pang; Evelyn Callaway; Beiyan Zhou; Ivan Ivanov; Robert S. Chapkin Molecular Basis of Disease 2017 (Accepted for publication)