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Keep Me Around: Intron Retention Detection and Analysis

Pimentel, Harold and Conboy, John G. and Pachter, Lior (2016) Keep Me Around: Intron Retention Detection and Analysis. . (Submitted) https://resolver.caltech.edu/CaltechAUTHORS:20170306-132431515

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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.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://arxiv.org/abs/1510.00696arXivDiscussion Paper
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.
Funders:
Funding AgencyGrant Number
NSF Graduate Research FellowshipUNSPECIFIED
NIHR01 DK094699
Record Number:CaltechAUTHORS:20170306-132431515
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170306-132431515
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74796
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:06 Mar 2017 21:34
Last Modified:03 Oct 2019 16:43

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