Errors using DADA2 after cutadapt

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. :laughing:

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.

Unfortunately there isn’t much we can do without this info. Please post:

  • the commands you ran
  • the full error messages (run with --verbose)
  • the version of QIIME 2 you are using

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