I observed a discrepancy for Illumina HiSeq 4000 SE 50 run. The Lane 7 had very low Phred Quality % bases compared to other two lanes belonging to same sample set. The %Q30 was in 50's while for others its >90%. The libraries are CHIPseq libraries.
The lanes 5 and 6 which have samples from the same project show good quality phred scores.
I delmultiplexed the run again using
--barcode-mismatches 0 but found no change in Phred Quality. When i tried using
--barcode-mismacthes 2, it gave an error
Barcode collision for barcodes: GGCTAC, AGTCAA
Is this a de-multiplexing error or a run error?