Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.

TitleHaplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
Publication TypeJournal Article
Year of Publication2011
AuthorsTurro E, Su S-Y, Gonçalves Â, Coin LJM, Richardson S, Lewin A
JournalGenome Biol
Volume12
Issue2
PaginationR13
Date Published2011
ISSN1465-6914
KeywordsAlgorithms, Allelic Imbalance, Alternative Splicing, Animals, Computational Biology, Gene Expression Profiling, Haplotypes, Humans, Mice, Models, Statistical, RNA, Messenger, Sequence Analysis, RNA, Software, Transcriptome
Abstract

We present a novel pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data. We achieve this by modeling the expression of haplotype-specific isoforms. If unknown, the two parental isoform sequences can be individually reconstructed. A new statistical method, MMSEQ, deconvolves the mapping of reads to multiple transcripts (isoforms or haplotype-specific isoforms). Our software can take into account non-uniform read generation and works with paired-end reads.

DOI10.1186/gb-2011-12-2-r13
Alternate JournalGenome Biol.
PubMed ID21310039