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Old 06-11-2015, 05:58 AM   #19
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Location: New York, NY

Join Date: Jun 2012
Posts: 5

Is there a way of efficiently using the BBMap tools to cut variable length and variable sequence primer pairs from amplicon sequencing data either pre-alignment (fastq) or post-alignment (BAM)? I am thinking in regards to RainDance and Fluidigm data where there are hundreds of amplicons, many of which overlap, each with different forward/reverse primers.
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