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Old 01-07-2015, 10:59 AM   #4
microgirl123
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Location: New England

Join Date: Jun 2012
Posts: 200
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I'm usually pooling 96 samples into a MiSeq run and sometimes a couple of them have very low amounts of reads. Possibly this is due to a quantification or pooling problem. Once in a while, it is so bad that I think it may be a case of miscalled indexes.

I've never noticed a link between faint gel bands and lower amounts of reads. I have, however, used samples that have no visible band on the gel and gotten the expected amount of reads back. Incidentally, what volume of your PCR product are you loading on the gel?

The only thing that I have seen reliably cause a problem is the presence of adapter (primer) dimers or more than one band on the gel.
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