Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

High-throughput sequencing of cDNA (RNA-seq) is used extensively to characterize the transcriptome of cells. Many transcriptomic studies aim at comparing either abundance levels or the transcriptome composition between given conditions, and as a first step, the sequencing reads must be used as the basis for abundance quantification of transcriptomic features of interest, such as genes or transc...

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences Supplementary Material

The sim2 data set consists of simulated sequencing reads from the human chromosome 1. The sequencing parameters as well as underlying TPM values for the 15,677 transcripts in one of the two simulated conditions were estimated using RSEM v1.2.21 [6] from the ERS326990 sample from the ArrayExpress data set with accession number E MTAB 1733. We simulated three biological replicates from each of tw...

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences [version 2; referees: 2 approved]

High-throughput sequencing of cDNA (RNA-seq) is used extensively to characterize the transcriptome of cells. Many transcriptomic studies aim at comparing either abundance levels or the transcriptome composition between given conditions, and as a first step, the sequencing reads must be used as the basis for abundance quantification of transcriptomic features of interest, such as genes or transc...

RNA-Seq workflow: gene-level exploratory analysis and differential expression

Here we walk through an end-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample. We will perform exploratory data analysis (EDA) for quality assessment and to e...

DRIMSeq: Dirichlet-multinomial framework for differential transcript usage and transcript usage QTL analyses in RNA-seq