Transcript length bias in RNA-seq data confounds systems biology

摘要: Several recent studies have demonstrated the effectiveness of deep sequencing for transcriptome analysis (RNA-seq) in mammals. As RNA-seq becomes more affordable, whole genome transcriptional profiling is likely to become platform choice species with good genomic sequences. yet, a rigorous methodology has not been developed and we are still stages exploring features data. We investigated effect transcript length bias data using three different published sets. For standard analyses aggregated tag counts each gene, ability call differentially expressed genes between samples strongly associated transcript. Transcript calling general feature current protocols technology. This implications ranking genes, particular may introduce gene set testing pathway other multi-gene systems biology analyses. article was reviewed by Rohan Williams (nominated Gavin Huttley), Nicole Cloonan Mark Ragan) James Bullard Sandrine Dudoit).