Format

Send to

Choose Destination
Bioinformatics. 2019 Jan 15;35(2):340-342. doi: 10.1093/bioinformatics/bty483.

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

Author information

1
Department of Developmental and Cell Biology, UC Irvine, Irvine, CA, USA.
2
Center for Complex Biological Systems, UC Irvine, Irvine, CA, USA.

Abstract

Motivation:

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.

Results:

Our method corrects nearly all mismatches and indels present in a publically available human PacBio Iso-seq dataset, and rescues 39% of noncanonical splice junctions.

Availability and implementation:

All Python and R scripts used in this paper are available at https://github.com/dewyman/TranscriptClean.

PMID:
29912287
PMCID:
PMC6329999
DOI:
10.1093/bioinformatics/bty483
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center