Hi everyone! I have a basic question, is there currently version of the rnaseq pipeline to process 3' based RNA sequencing? Like just for gene expression quantification

The rnaseq pipeline gives you counts tables. What you do with them is really where it matters if your reads come from random fragmentation or 3'-end sequencing. You can try to optimize parameters during the run (discussed and attempted in this post), but I'm not sure how necessary that is (besides correct UMI processing, if applicable), or what the right way is (you can experiment with that, I've never used 3' data for bulk RNAseq). What is more important is which output to use -- you get raw counts, as well as a couple of versions of the table that are "bias corrected" using transcript length information (I think this is the same whether you are using alignment with STAR plus Salmon quantification or pseudo alignment). I always use the raw counts matrix, because the "corrections" have minor benefits in most cases, whereas in corner cases they can do crazy stuff, so for me the cost-benefit ratio is not good. For 3'-end sequences, you must use the raw counts, because transcript length is not part of the equation for this technology and any correction based on it makes no sense and would be detrimental. Any downstream statistics should be the same as usual. Where you'll probably see some differences is the QC output, so look at that critically and keep in the peculiarities of the technology in mind (e.g., the gene coverage would look very different). 🤞

Thanks a lot for the answer and pointing out the thread!