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Old 09-24-2018, 06:00 AM   #6
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
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As I see the dropoff after around 100 bases, I should also see that as the true insert length, right?
While likely let us hope that is not the case because otherwise you would be losing a lot of data to adapters and would have short reads.

When you have had a chance to investigate let us know what the FastQC profiles and the BBMap insert sizes look like.

Is this a MiSeq you have control over/physical access to? It may be worth having Illumina tech support take a look at this run remotely. They can diagnose if there was a hardware issue that led to the Q-score drop. If you have a maintenance contract they will likely replace the reagents at no charge in that case.
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