This is a follow-up to my question about make.contigs.
While checking a random sample of reads at each stage of Mothur, I found about half where a forward primer exact match is not present in the make.contigs output. For these reads, pcr.seqs typically trims something even though I have specified 0 mismatches in the pcr.seqs command. It usually grabs a small segment of sequence just before the reverse primer.
In addition, in some of the reads the forward primer exact match was present but pcr.seqs did not capture the entire sequence between the forward and reverse primers. It only captures a portion of it.
I have this data in an Excel spreadsheet, so I can email it to you if you want to take a closer look. I can’t really post it here in any nice format.
Here’s the pcr.seqs command I run: