Just a general question regarding how make.contigs command removes primers and barcodes
so we use oligos option with make.contigs to remove barcodes and primers. Our command is:
make.contigs(file=batch_file, oligos=oligos_file, bdiffs=0, pdiffs=0, checkorient=t, insert=25, trimoverlap=f, allfiles=0)
I found this quote from Sarah (in a previous post) “The make.contigs command is more strict about where primers can be located in the read. The make.contigs command will look for the barcodes and primers ONLY at the ends of the read. If the primers are found, they are removed and the fragments are assembled”
So, in our case, since we specify pdiffs=0, bdiffs=0, mothur will require that it sees the full sequences of both primers and barcodes at the very ends of the read. If they’re both found, they’re are removed and the sequences left are merged. Otherwise, both R1 and R2 will be scrapped.
Is that correct ? Curious to know if by any chance that some primers might still be found in the merged reads ? possible ?
Thank you for your help.