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Old 07-29-2019, 03:09 PM   #1
Jayson H
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Location: Salt Lake City

Join Date: Aug 2011
Posts: 1
Default FASTQ changing quality score to zero for primer sequences

I want to mask primer sequences from analysis, but I want to keep the sequences in the FASTQ to help with alignment. Searching against a primer list and changing the quality scores to zero for matching bases would effectively prevent those bases from being included in analysis, and the preserved bases would aid in aligning the target sequence. Is there a method or tool to do this?
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