Keep Me Around: Intron Retention Detection and Analysis
Genomics
2015-10-05 v1
Abstract
We present a tool, keep me around (kma), a suite of python scripts and an R package that finds retained introns in RNA-Seq experiments and incorporates biological replicates to reduce the number of false positives when detecting retention events. kma uses the results of existing quantification tools that probabilistically assign multi-mapping reads, thus interfacing easily with transcript quantification pipelines. The data is represented in a convenient, database style format that allows for easy aggregation across introns, genes, samples, and conditions to allow for further exploratory analysis.
Cite
@article{arxiv.1510.00696,
title = {Keep Me Around: Intron Retention Detection and Analysis},
author = {Harold Pimentel and John G. Conboy and Lior Pachter},
journal= {arXiv preprint arXiv:1510.00696},
year = {2015}
}