I have rna seq samples which show 3' bias in the gene body coverage of 10,000 random genes.
I first looked at the RIN values to see if degradation was linked to this, but all my samples are over 8 RIN, so I do not think it is the main reason.
I also read that different protocols might show different gene body coverage profiles. In this case we did mRNA seq (as opposed to total RNA seq).
However, a biological subgroup of the samples (plus a sample from another group) shows a significantly more pronounced bias.
Has anyone observed this before? Is there any way to correct for this bias in the counts? I am not sure whether this could cause false positives, as all samples of one biological group have the most pronounced bias.