I have recently joined a sequencing facility, and came across a problem that seems to frequently creep up in their Illumina HiSeq1000 - Significant differences in readcounts for libraries loaded on the same lane. Sometimes, the differences are quite large (16M for replicate 1 and 31M for replicate 2, for example). Can anyone tell me if this is normal, and a probable reason for why this should happen?
Thanks.
Thanks.
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