I am struggling with some bulk RNAseq data. I've been given the count matrix and metadata of bulk RNAseq which was run onto sorted T cells. Now the issue is that we unfortunately did not find what we would expect. I know that this happens most of the time in research, however I am looking if something went wrong during the sequencing or even before. Who run the analysis shared an excel file of their results report and I've noticed that for 10 out of 109 samples they had RIN values < 6 (3 of which had RIN = 1 and 1 had a RIN = 2.5). Nonetheless they procedeed with the sequencing for all of our samples. Do you think I should remove those samples? I've run a PCA to see if the majority the variance is associated with RIN score, but it does not seem so. Additionally I've looked at the multiQC report and I'd like to know if the plot of sequence duplication levels should be a concern or not.
Studying a bit about multiQC and FASTAQC report it's a bad output, but how bad?