First of all, thanks so much for making this pipeline. It's incredibly helpful!
I wanted to use my results with IsoformSwitchAnalyzeR, and it seems preferable to provide stats directly from the wf-transcriptomes results rather than allow ISA to recalculate TPM. This is because downstream analyses will not have access to read length for appropriate correction. However, I noticed that wf-transcriptomes converts TPM to integers before reporting. If I understand correctly, this makes them unsuitable for further analysis. Why is this? Am I missing something?
First of all, thanks so much for making this pipeline. It's incredibly helpful!
I wanted to use my results with IsoformSwitchAnalyzeR, and it seems preferable to provide stats directly from the wf-transcriptomes results rather than allow ISA to recalculate TPM. This is because downstream analyses will not have access to read length for appropriate correction. However, I noticed that wf-transcriptomes converts TPM to integers before reporting. If I understand correctly, this makes them unsuitable for further analysis. Why is this? Am I missing something?