SQUID: transcriptomic structural variation detection from RNA-seq.
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ABSTRACT:
SUBMITTER: Ma C
PROVIDER: S-EPMC5896115 | biostudies-literature | 2018 Apr
REPOSITORIES: biostudies-literature
Publications
SQUID: transcriptomic structural variation detection from RNA-seq.
Ma Cong C Shao Mingfu M Kingsford Carl C
Genome biology 20180412 1
Transcripts are frequently modified by structural variations, which lead to fused transcripts of either multiple genes, known as a fusion gene, or a gene and a previously non-transcribed sequence. Detecting these modifications, called transcriptomic structural variations (TSVs), especially in cancer tumor sequencing, is an important and challenging computational problem. We introduce SQUID, a novel algorithm to predict both fusion-gene and non-fusion-gene TSVs accurately from RNA-seq alignments. ...[more]
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