How many mismatches one can allow for the barcodes length greater than 8 while making the contigs? Here I am talking about Miseq 16sRNA data.
I generally consider no mismatch for the primers, but 1 mismatch for barcodes of a longer size.
Marie-Claire Arrieta
I don't think there is a science to that. If you look at the SOP for 16S bioinformatic analysis using Mothur, for example, they use 1 mismatch for barcodes and 2 for primers. I personally use 1 for each.
I've gotten used to running a control mock community along with all my samples and this allows me to trust the sequencing results I am getting.
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