TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts | Zendy

Dana Wyman | Zendy; A Mortazavi | Zendy

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TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts

Author(s) -

Dana Wyman,

A Mortazavi

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty483

Subject(s) - splice , indel , python (programming language) , computational biology , computer science , exon , rna splicing , gene isoform , scripting language , genetics , alternative splicing , biology , genome , gene , rna , programming language , single nucleotide polymorphism , genotype

Long-read, single-molecule sequencing platforms hold great potential for isoform discovery and characterization of multi-exon transcripts. However, their high error rates are an obstacle to distinguishing novel transcript isoforms from sequencing artifacts. Therefore, we developed the package TranscriptClean to correct mismatches, microindels and noncanonical splice junctions in mapped transcripts using the reference genome while preserving known variants.

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