SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty

Detecting allelic imbalance at the isoform level requires accounting for inferential uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW, uses Salmon and Swish to offer analysis at various levels of resolution, including gene, isoform, and aggregating isoforms to group...

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Bibliographic Details
Published in:Genome Biology 2023-07, Vol.24 (1), p.165-21, Article 165
Main Authors: Wu, Euphy Y, Singh, Noor P, Choi, Kwangbom, Zakeri, Mohsen, Vincent, Matthew, Churchill, Gary A, Ackert-Bicknell, Cheryl L, Patro, Rob, Love, Michael I
Format: Article
Language:English
Subjects:
Allelic Imbalance
Genes
Genomes
Isoforms
Protein Isoforms - genetics
RNA-Seq
Simulation
Software
Statistical inference
Transcription initiation
Transcription Initiation Site
Uncertainty
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Summary:Detecting allelic imbalance at the isoform level requires accounting for inferential uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW, uses Salmon and Swish to offer analysis at various levels of resolution, including gene, isoform, and aggregating isoforms to groups by transcription start site. The aggregation strategies strengthen the signal for transcripts with high uncertainty. The SEESAW suite of methods is shown to have higher power than other allelic imbalance methods when there is isoform-level allelic imbalance. We also introduce a new test for detecting imbalance that varies across a covariate, such as time.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-023-03003-x