This README is intended to provide the necessary steps to reproduce the results, files and figures included in the following publication:
The discovery potential of RNA processing profiles
Amadís Pagès, Ivan Dotu, Joan Pallarés-Albanell, Eulàlia Martí, Roderic Guigó and Eduardo Eyras
Git - http://git-scm.com/
Perl - https://www.perl.org/get.html
Python - https://www.python.org/downloads/
R - https://www.r-project.org/
BEDTools - https://github.com/arq5x/bedtools2/releases/latest
SRA Toolkit - http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
SeRPeNT - https://bitbucket.org/regulatorygenomicsupf/serpent/downloads
STAR - https://github.com/alexdobin/STAR/releases
Infernal - http://eddylab.org/software/infernal/
cutadapt - https://github.com/marcelm/cutadapt
git clone https://amadis_pages@bitbucket.org/regulatorygenomicsupf/serpent-analysis.git
cd serpent-analysis
Edit mks/mkdefs.makefile to set up software dependencies
make benchmarking
make annotation
make diffproc