TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads

[1] Wang Z(2009)RNA-Seq: a revolutionary tool for transcriptomics Nature reviews Genetics 10 57-63

[2] Gerstein M(2012)Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nature protocols 7 562-578

[3] Snyder M(2008)Mapping and quantifying mammalian transcriptomes by RNA-Seq Nature methods 5 621-628

[4] Trapnell C(2010)RNA-Seq gene expression estimation with read mapping uncertainty Bioinformatics (Oxford, England) 26 493-500

[5] Roberts A(2013)TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference Bioinformatics (Oxford, England) 29 (18):2292-2299

[6] Goff L(2011)RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome BMC bioinformatics 12 323-1760

[7] Pertea G(2012)A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers BMC genomics 13 341-359

[8] Kim D(2013)Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data PLoS computational biology 9 e1003031-65

[9] Kelley DR(2009)Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics (Oxford, England) 25 1754-652

[10] Pimentel H(2012)Fast gapped-read alignment with Bowtie 2 Nature methods 9 357-510

[1] Wang Z(2009)RNA-Seq: a revolutionary tool for transcriptomics Nature reviews Genetics 10 57-63

[2] Gerstein M(2012)Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nature protocols 7 562-578

[3] Snyder M(2008)Mapping and quantifying mammalian transcriptomes by RNA-Seq Nature methods 5 621-628

[4] Trapnell C(2010)RNA-Seq gene expression estimation with read mapping uncertainty Bioinformatics (Oxford, England) 26 493-500

[5] Roberts A(2013)TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference Bioinformatics (Oxford, England) 29 (18):2292-2299

[6] Goff L(2011)RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome BMC bioinformatics 12 323-1760

[7] Pertea G(2012)A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers BMC genomics 13 341-359

[8] Kim D(2013)Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data PLoS computational biology 9 e1003031-65

[9] Kelley DR(2009)Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics (Oxford, England) 25 1754-652

[10] Pimentel H(2012)Fast gapped-read alignment with Bowtie 2 Nature methods 9 357-510