We recently received paired end results sequenced on the HiSeq 2500, and the forward reads are good but the reverse reads are of extremely low quality (.1% pass generous quality filtering thresholds).
I've attached the FastQC results for the forward (R1) and reverse (R2) reads (let me know if you can't access them). My question is- has anyone seen this issue before? I think it is strange that the R1 reads are so good and the R2 reads are so bad. What would you attribute this to? Overclustering on the flowcell? Something wrong during library prep?
Thanks in advance!
I've attached the FastQC results for the forward (R1) and reverse (R2) reads (let me know if you can't access them). My question is- has anyone seen this issue before? I think it is strange that the R1 reads are so good and the R2 reads are so bad. What would you attribute this to? Overclustering on the flowcell? Something wrong during library prep?
Thanks in advance!
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