Closed JamalEH closed 4 years ago
Yes you can use the counts with DESeq. The .tpm.gz files are calculated using EM across annotated transcripts with all reads, that is exon-body and junction reads.
Also this info is in the paper -- https://doi.org/10.1016/j.molcel.2018.08.018
Hi,
Can I perform differential expression analysis at gene and isoform level using DESeq2 on the count matrix from the .tpm.gz files generated by whippet? Can you also please tell me how the counts are calculated, based on junction reads?
Thank you in advance! Best regards, Jamal.