Update rMATS - Githubissues

TheJacksonLaboratory / splicing-pipelines-nf

Repository for the Anczukow-Lab splicing pipeline

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Update rMATS #312

Closed angarb closed 1 year ago

angarb commented 2 years ago

Problem

rMATS has been updated with release of 4.1.2 (we are currently using 4.1.1).

rMATS upgrades:

Improve the performance of the FDR calculation
Pass --nthread to STAR if starting with FASTQ files
Add STAR to the Dockerfile
Allow using string IDs for events with --fixed-event-set
Remove buffer size limits in statistical model
Handle Windows line endings
Handle file systems that do not support colon in filenames
Bug fix of single-end strand checking
Bug fix of integer overflow for read outcome counts

The bug fixes and improved FDR calculation are most relevant to us.