Copyright 2014 Dmitri Pervouchine (email@example.com), 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/.
Integrative Pipeline for Splicing Analyses (IPSA)
** This is a full version. A short version is available here https://github.com/pervouchine/ipsa**
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.
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
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/)
Perl standard modules (http://www.perl.org/)
To install, do
git clone https://github.com/pervouchine/ipsa-full cd ipsa-full make all
An example of a pipeline buildout is available by running
make -f example.mk all
The documentation on the pipeline components is available in latex/ subdirectory The documentation on the sjcount utility is available in sjcount/latex/ subdirectory