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Published March 6, 2017 | Submitted
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Keep Me Around: Intron Retention Detection and Analysis

Abstract

We present a tool, keepme 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.

Additional Information

Submitted on 2 Oct 2015. October 5, 2015 HP was supported by the NSF GRFP. JGC and LP were supported in part by NIH R01 DK094699.

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August 20, 2023
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