So I got the multiqc report for the CCC Acer samples to work, and it seems like they are all over the place.

Note: these files have not been trimmed in any way.

I need to double-check they are 3’ RNA-Seq and what kind of sequencing they were done on. (going to look at Natalia’s presentation)

It is 3’ Quantseq RNA sequencing

Also a note from Natalia: the Novaseq S2 brings a lot of “artifacts” that need to be trimmed out. PolyA tail can be really long, even post-trimming, so that compromises alignment.

She recommends using TrimGalore and use a code specifically to remove artifacts from NovaSeq + PolyA tails.

So, let’s try trimming them and then see if the FastQC results below become better (before we try to interpret these results below).