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Fusion detection and quantification by pseudoalignment

Melsted, Páll and Hateley, Shannon and Joseph, Isaac Charles and Pimentel, Harold and Bray, Nicolas and Pachter, Lior (2017) Fusion detection and quantification by pseudoalignment. . (Unpublished) http://resolver.caltech.edu/CaltechAUTHORS:20181029-134221299

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Abstract

RNA sequencing in cancer cells is a powerful technique to detect chromosomal rearrangements, allowing for de novo discovery of actively expressed fusion genes. Here we focus on the problem of detecting gene fusions from raw sequencing data, assembling the reads to define fusion transcripts and their associated breakpoints, and quantifying their abundances. Building on the pseudoalignment idea that simplifies and accelerates transcript quantification, we introduce a novel approach to fusion detection based on inspecting paired reads that cannot be pseudoaligned due to conflicting matches. The method and software, called pizzly, filters false positives, assembles new transcripts from the fusion reads, and reports candidate fusions. With pizzly, fusion detection from raw RNA-Seq reads can be performed in a matter of minutes, making the program suitable for the analysis of large cancer gene expression databases and for clinical use. pizzly is available at https://github.com/pmelsted/pizzly.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/166322DOIDiscussion Paper
ORCID:
AuthorORCID
Melsted, Páll0000-0002-8418-6724
Pachter, Lior0000-0002-9164-6231
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. bioRxiv preprint first posted online Jul. 20, 2017. The authors would like to thank David P. Kreil and Paweł P. Łabaj for helpful feedback.
Record Number:CaltechAUTHORS:20181029-134221299
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20181029-134221299
Official Citation:Fusion detection and quantification by pseudoalignment. Páll Melsted, Shannon Hateley, Isaac Charles Joseph, Harold Pimentel, Nicolas L Bray, Lior Pachter. bioRxiv 166322; doi: https://doi.org/10.1101/166322
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:90472
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:30 Oct 2018 01:57
Last Modified:30 Oct 2018 01:57

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