Hi,
I am using paired - end data and trimmed primer sequences using --p-front-f / --p-front-r with the cutadapt plugin. With my resulted trimmed-seqs.qza I went ahead and executed DADA2 but returned with an error.
I won't post the whole thing here but there is a ^ sign that is generated after executing cut-adapts parameters --p-front-f / --p-front-r. DADA2 is saying that is preventing it from continuing. I read under the docs for --p-front-f/r:
If a
^
character is prepended, the adapter is only found if it is at the beginning of the read.
To work around this, I decided to use --p-anywhere-f/r but a lot of primer sequences were not removed. Most of them are at the beginning of feature sequences after DADA2 while observing rep-seqs. Is there any way I can execute --p-front-f/r without having the ^ character present?
This may be an issue because I should be using --p-adaptor-f/r but I am getting the same failure when I use it that many have gotten on this forum due to an apparent bug. I was trying to find a work - around before I went on to using cutadapt itself.
The primers that were used:
F: 5′-CCTACGGGNGGCWGCAG-3′
R: 5′-GACTACHVGGGTATCTAATCC-3
Lastly, would a solution be to simply trim-left-f/r the number of base pairs that these primer sequences have? (Under DADA2) I will attempt that now.
Any advice would be much appreciated.