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Old 11-23-2015, 09:23 AM   #1
Location: Los Angeles, CA

Join Date: Dec 2014
Posts: 30
Default Strand bias in amplicon sequencing

I am seeing random strand bias in amplicon reads on an Illumina MiSeq run. Some of the amplicons have effectively complete dropout of the forward or reverse read. This occurs across every sample on the run.

I have used this library prep kit before and did not see these results before. Also, the bias occurs in regions that I would not expect this to happen (50% GC).

Has anyone seen this before or have any ideas what could be causing this? Is there anything in the library prep process that might cause this?
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