mothur

Make.contigs barcode question

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?

M00278_49_000000000-CPBKN_1_1108_23033_3567 | b(b) ee=6.87543 fbdiffs=3(noMatch), rbdiffs=1001(noMatch) fpdiffs=0(match), rpdiffs=0(match)

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.

Thank you for your kindly reply

Welcome to the mothur community! This is a very good question. I added a section to the make.contigs page to explain this better as I suspect others could benefit, https://mothur.org/wiki/Make.contigs#oligos_scrap_code_meanings.

  • 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.

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.