title: Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
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.
authors.affiliation: Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, W2 1PG, UK. ernest.turro@ic.ac.uk
authors.forename: Ernest
authors.initials: E
authors.lastname: Turro
authors.forename: Shu-Yi
authors.initials: SY
authors.lastname: Su
authors.forename: Ângela
authors.initials: Â
authors.lastname: Gonçalves
authors.forename: Lachlan J M
authors.initials: LJ
authors.lastname: Coin
authors.forename: Sylvia
authors.initials: S
authors.lastname: Richardson
authors.forename: Alex
authors.initials: A
authors.lastname: Lewin
mesh_terms: D000465:Algorithms; D022981:Allelic Imbalance; D017398:Alternative Splicing; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D006239:Haplotypes; D006801:Humans; D051379:Mice; D015233:Models, Statistical; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger