Transcriptome splicing analysis tools

Question

[Morris_Chair]

Dear all,

I have a question regarding RNA-seq data analysis. Do you know which tool(s) within the RStudio environment can be used to examine splicing differences across all transcripts not just for a single gene?

Thank you in advance for your help!

Answer 1

[michael.ante]

Hi,

When I still worked with transcriptomics, I used DEXSeq to perform differential exon usage. You need aligned BAM files and the transcript annotation (see here for more details).