@article {Alamancos008763, author = {Gael P. Alamancos and Amad{\'\i}s Pag{\`e}s and Juan L. Trincado and Nicol{\'a}s Bellora and Eduardo Eyras}, title = {SUPPA: a super-fast pipeline for alternative splicing analysis from RNA-Seq}, elocation-id = {008763}, year = {2014}, doi = {10.1101/008763}, publisher = {Cold Spring Harbor Laboratory}, abstract = {High-throughput RNA sequencing allows genome-wide analyses of pre-mRNA splicing across multiple conditions. However, the increasing number of available datasets represents a major challenge in terms of time and storage required for analyses. Here we describe SUPPA, a computational pipeline to calculate relative inclusion values of alternative splicing events, exploiting fast transcript quantification of a known annotation. SUPPA provides a fast and accurate approach to calculate inclusion levels of alternative splicing events from a large number of samples, thereby facilitating systematic analyses in the context of large-scale projects using limited computational resources. SUPPA is available at https://bitbucket.org/regulatorygenomicsupf/suppa under the MIT license and is implemented in Python 2.7.}, URL = {https://www.biorxiv.org/content/early/2014/09/04/008763}, eprint = {https://www.biorxiv.org/content/early/2014/09/04/008763.full.pdf}, journal = {bioRxiv} }