Computational protocol: Computational identification and validation of alternative splicing in ZSF1 rat RNA seq data, a preclinical model for type 2 diabetic nephropathy

Similar protocols

Protocol publication

[…] Raw sequencing reads were processed by Salmon 0.8.2 using Ensembl v87 rat annotation with default options. The resulting isoform-level counts tables were analysed using the R/Bioconductor package edgeR 3.16.5 for normalization and differential expression between lean and obese groups at each time point. The quasi-likelihood F-test glmQLFit was used instead of a likelihood ratio test because of the relatively small numbers of replicates at each time point. [...] Raw sequencing reads were first mapped to the rat genome using STAR 2.5.2a with the 2-PASS option. The resulting 2-PASS bam files were processed by rMATS for exon inclusion level differences between lean and obese groups at each time point. Both exon–exon junction reads and the reads that mapped to the exons were used in the analyses. The resulting alternative splicing tables in five categories (alternative 5′ splice site, alternative 3′ splice site, mutually exclusive exons, retained introns, and skipped exons) were merged. […]

Pipeline specifications

Software tools edgeR, STAR, rMATS
Application RNA-seq analysis
Organisms Rattus norvegicus, Homo sapiens
Diseases Diabetic Nephropathies