I used make.contigs to merger read.1 and read.2. I also provided barcode oligos to separate samples. Both the forward and reverse barcode included 8 nucleotides. In the scarp fasta file, I got the following sequence. May I ask the meaning of “rbdiffs=1001(noMatch)”. Does it mean the reverse barcode absent in the sequence?
The other question is the meaning of “fbdiffs=0(noMatch), rbdiffs=3(noMatch)”.
Does it mean that forward barcode is matched but there were 3 mismatches in the reverse barcode? Therefore, this sequence was discarded.
fbdiffs=3(noMatch) - mothur found a barcode, but the number of diffs=3, bdiffs=1 so no match is found.
rbdiffs=1001(noMatch) - 1001 indicates the reverse barcode was not searched for because the forward barcode was not found. (1000+bdiffs) = 1001 - no search and noMatch.
fpdiffs=0(match) - perfect match to forward primer or no primers in oligos file.
rpdiffs=0(match) - perfect match to reverse primer or no primers in oligos file.