In:
Bioinformatics, Oxford University Press (OUP), Vol. 32, No. 1 ( 2016-01-01), p. 43-49
Abstract:
Motivation: Discovery of novel splicing from RNA sequence data remains a critical and exciting focus of transcriptomics, but reduced alignment power impedes expression quantification of novel splice junctions. Results: Here, we profile performance characteristics of two-pass alignment, which separates splice junction discovery from quantification. Per sample, across a variety of transcriptome sequencing datasets, two-pass alignment improved quantification of at least 94% of simulated novel splice junctions, and provided as much as 1.7-fold deeper median read depth over those splice junctions. We further demonstrate that two-pass alignment works by increasing alignment of reads to splice junctions by short lengths, and that potential alignment errors are readily identifiable by simple classification. Taken together, two-pass alignment promises to advance quantification and discovery of novel splicing events. Contact: arul@med.umich.edu, nesvi@med.umich.edu Availability and implementation: Two-pass alignment was implemented here as sequential alignment, genome indexing, and re-alignment steps with STAR. Full parameters are provided in Supplementary Table 2. Supplementary information: Supplementary data are available at Bioinformatics online.
Type of Medium:
Online Resource
ISSN:
1367-4811
,
1367-4803
DOI:
10.1093/bioinformatics/btv642
Language:
English
Publisher:
Oxford University Press (OUP)
Publication Date:
2016
detail.hit.zdb_id:
1468345-3
SSG:
12
Bookmarklink
