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Old 09-04-2017, 07:34 AM   #1
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Location: Western Europe

Join Date: Nov 2013
Posts: 9
Question Assembling mini barcodes into full-length gene

I have metabarcoding reads from an Illumina MiSeq run. I usually use a primer set which amplifies a certain fragment of COI. Now, however, we have used three different primer sets which produce overlapping fragments. My question is, is it possible to first merge the paired ends from each primer, and then assemble the fragments together, and then continue with the usual metabarcoding pipeline? I find much information online about merging paired-ends, but not about incorporating longer contigs. I'm a grad student, instructed to investigate this, and I wanted to ask around here first, before I waste a lot of time trying to do this if my efforts are misguided. Thanks.
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