Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching

[1] Wang Z(2009)RNA-Seq: a revolutionary tool for transcriptomics Nat Rev Genet 10 57-63

[2] Gerstein M(2011)Computational methods for transcriptome annotation and quantification using RNA-seq Nat Methods 8 469-477

[3] Snyder M(2012)Tools for mapping high-throughput sequencing data Bioinformatics 28 3169-3177

[4] Garber M(2012)Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads Bioinformatics 28 2914-2921

[5] Grabherr MG(2013)TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome Biology 14 R36-21

[6] Guttman M(2013)STAR: ultrafast universal RNA-seq aligner Bioinformatics 29 15-R106

[7] Trapnell C(2010)Differential expression analysis for sequence count data Genome Biol 11 R106-14

[8] Fonseca NA(2004)Bioconductor: open software development for computational biology and bioinformatics Genome Biol 5 R80-53

[9] Rung J(2012)GenomicRanges: representation and manipulation of genomic intervals R Package Version 1 12-4297

[10] Brazma A(2012)Differential analysis of gene regulation at transcript resolution with RNA-seq Nat Biotechnol 31 46-2017

[1] Wang Z(2009)RNA-Seq: a revolutionary tool for transcriptomics Nat Rev Genet 10 57-63

[2] Gerstein M(2011)Computational methods for transcriptome annotation and quantification using RNA-seq Nat Methods 8 469-477

[3] Snyder M(2012)Tools for mapping high-throughput sequencing data Bioinformatics 28 3169-3177

[4] Garber M(2012)Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads Bioinformatics 28 2914-2921

[5] Grabherr MG(2013)TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome Biology 14 R36-21

[6] Guttman M(2013)STAR: ultrafast universal RNA-seq aligner Bioinformatics 29 15-R106

[7] Trapnell C(2010)Differential expression analysis for sequence count data Genome Biol 11 R106-14

[8] Fonseca NA(2004)Bioconductor: open software development for computational biology and bioinformatics Genome Biol 5 R80-53

[9] Rung J(2012)GenomicRanges: representation and manipulation of genomic intervals R Package Version 1 12-4297

[10] Brazma A(2012)Differential analysis of gene regulation at transcript resolution with RNA-seq Nat Biotechnol 31 46-2017