Current Bioinformatics Seminar
Time: 11AM Tuesdays.
Venue: Davis Auditorium and Online
23 April 2024
Applying edgeR for alternative splicing analysis
Lizhong ChenWEHI Bioinformatics
edgeR is an R package for analyzing sequence read count data from genomic sequencing technologies such as RNA-seq, ChIP-seq and ATAC-seq, using negative binomial generalized linear models. The new quasi-likelihood differential expression pipeline has been implemented in the recent update, edgeR 4.0. It agrees with the current edgeR approach when low counts are filtered, but it proves very accurate for a much wider range of datasets, including small count datasets without low count filtering, which is essential to differential exon usage analysis for alternative splicing. In this talk, I will provide an exploratory differential exon usage analysis of Foxp1 data using diffSplice from edgeR and limma and show the advantages of the new QL method without low count filtering. Also, some related topics like alignment, exon-exon junction, reference genome and simulation problem will be discussed.