can I use .tpm.gz files to perform gene/transcript differential expression analysis?

timbitz / Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level

MIT License

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can I use .tpm.gz files to perform gene/transcript differential expression analysis? #91

Closed JamalEH closed 4 years ago

JamalEH commented 4 years ago

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.

timbitz commented 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.

timbitz commented 4 years ago

Also this info is in the paper -- https://doi.org/10.1016/j.molcel.2018.08.018