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CancerRNASeq

##What is CancerRNAseq? CancerRNAseq is a pipeline for transcriptomics datasets. CancerRNAseq is implemented in Perl and uses R to generate various figures to visulaize the results and consists of three modules: (i) preprocessing, (ii) mapping and (iii) analysis and visualization.

The proprocessing consists of an adapter trimming, a quality trimming and a sequencing error correction step with three successively executed tools (CutAdapt, Trimmomatic and rCorrector). In the mapping step one of three alignment tools (TopHat2, HISAT2 or STAR) can be chosen to map the preprocessed reads to the reference genome. The calculation of differentially expressed transcripts with the Cufflinks suite (Cufflinks, Cuffmerge and Cuffdiff) as well as to generate graphics of the resulting gene lists is performed in the analysis and visualization step.

##Install

  1. Clone the GitHub repo, e.g. git clone https://github.com/RaphaelHablesreiter/CancerRNASeqPipeline
  2. To run CancerRNAseq call the CancerRNASeq.pl-file, e.g. $ perl CancerRNASeq.pl -config /path/to/file/userconfig.ini)

##Usage

CancerRNAseq is a command line tool that can be executed by calling the CancerRNASeq.pl-file with the ability to add parameters directly to the execution command (e.g., $ perl CancerRNASeq.pl -config /path/to/file/userconfig.ini -silent -overwrite -threads 20).

Paramaters that can be added to the execution command of CancerRNAseq are:

  • config <User Configuration File>
  • help
  • overwrite (default = FALSE)
  • silent (default = FALSE)
  • threads <Number of threads> (default = 1)

The only necessary parameter to execute the pipeline successfully is the path to the user configuration file in INI-format (e.g., $ perl CancerRNASeq.pl -config /path/to/file/userconfig.ini). This file contains information such as input file paths and user parameters (example user configuration file is attached).

##Output

CancerRNAseq creates a folder with the user name, containing subfolders with all the intermediate files and results for the pipeline run.

##Terms of use

Copyright (C) 2017 Raphael Hablesreiter

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.