pervouchine / ipsa-full

Integrative Pipeline for Splicing Analyses (IPSA)

Copyright 2014 Dmitri Pervouchine ([email protected]), Lab Roderic Guigo Bioinformatics and Genomics Group @ Centre for Genomic Regulation Parc de Recerca Biomedica: Dr. Aiguader, 88, 08003 Barcelona

This file is a part of the 'ipsa-full' package. 'ipsa-full' package 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.

'ipsa-full' package 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 'ipsa-full' package. If not, see http://www.gnu.org/licenses/.

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Integrative Pipeline for Splicing Analyses (IPSA)

** This is a full version. A short version is available here https://github.com/pervouchine/ipsa**

• DISCLAIMER

  Software and documentation in this release are very preliminary. Currently the pipeline is configured to download a few BAM files and run all computations for them, as an example.

• SYNOPSIS

The integrative pipeline for splicing analyses does:

• Quantification of splice junctions and splice boundaries

• Calculation of splicing indices, exon- and intron-centric

• Analysis of micro-exons and local splice-graph structure

• DEPENDENCIES

• maptools (automatic from https://github.com/pervouchine/maptools)

• sjcount (automatic from https://github.com/pervouchine/sjcount)

• samtools (needed by sjcount, automatic from http://sourceforge.net/projects/samtools/files/samtools/0.1.18/)

• R-statistics (http://www.r-project.org/)

• ggplot2 (http://ggplot2.org/)

• Perl standard modules (http://www.perl.org/)

• INSTALLATION

To install, do

git clone https://github.com/pervouchine/ipsa-full
cd ipsa-full
make all

• EXAMPLES

An example of a pipeline buildout is available by running

make -f example.mk all

• DOCUMENTATION

The documentation on the pipeline components is available in latex/ subdirectory The documentation on the sjcount utility is available in sjcount/latex/ subdirectory