we are having some trouble with our chip-seq experiment. we're sequencing yeast in a paired-end mode (2X76b length), we have eight samples with four biological replicates. The samples were barcoded and multiplexed over the four lanes of a flow cell.
the quality of the data is not as good as we would like it to be, but what I am wondering most is the fact, that the reads from the reverse strand (R2) show a much lesser quality than the forward strand (R1) reads. And this is consistent over all eight samples.
I don't think this is a lane-specific problem. As you can see in the attached pictures below, the forward strand (R1) looks better than the reverse strand (R2) independent of the lane and or sample.
As I can't think of any biological solution for the problem (is there?), I would appreciate if someone has already encountered this kind of problems with his/her data and can share the experience. Is there a technical problem here?