Is the raw counts file that I’d use for something like DESeq2 the one that's found in the rsem_star folder? It looks like there are a few versions there, so I'm not sure which is which. There's also a count file in the deseq2 qc folder (alongside a vst dataset). What's the difference between all of the count files? I just want to make sure I'm using the right one for downstream analyses. Same with tpm files, it looks like there are a couple and I'm not sure what the differences are. Does anyone have any insight about this? Thanks!

There's some instructions here about what files to use: https://nf-co.re/rnaseq/3.26.0/docs/output/#pseudoalignment They're salmon, but you'll find RSEM files matching the same patterns in recent pipeline verisons.

Thank you!