Current Bioinformatics Seminar
Time: 11AM Tuesdays.
Venue: Davis Auditorium and Online
30 July 2024
This is a WEHI only event.Explore human transcriptome using the T2T reference and edgeR 4.0
Xueyi DongWEHI Bioinformatics/ACRF CBSC
The human T2T-CHM13 genome assembly provides unprecedented accuracy and completeness, offering invaluable insights into various research fields including transcriptomics. However, current gene annotations of T2T-CHM13 reference genome do not follow universal standards in format, which brings challenges in transcriptomics analysis. Here, we present a pipeline for RNA-seq differential transcript expression and differential transcript usage analysis using T2T-CHM13 reference and edgeR version 4.0. The R/Bioconductor packages GenomicRanges and rtracklayer were used to efficiently organize T2T-CHM13 gene and transcript annotation information from GFF files. With the recent release of edgeR version 4, new statistical approaches have been applied in the pipeline to improve the performance. Using this pipeline, we analyzed an RNA-seq dataset of human naive CD4+ T cells at 3 different time points after activation from 10 healthy donors. The results show that we can effectively detect meaningful differential splicing transcripts using this pipeline.