Plugin error from dada2 trying to truncate and denoise after trimming primers with cutadapt

[lizgehret]

Hi @microbiotaphyto,

Thanks for your patience here!

@microbiotaphyto

Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) :
  Input must be a valid sequence table.
Calls: removeBimeraDenovo -> isBimeraDenovoTable
Execution halted

This error essentially means that your reads were not able to be merged. This is typically due to trim/trunc settings that have removed too many reads, which will produce an insufficient overlap between your forward/reverse reads - hence, preventing any merging from occurring.

My first recommendation here would be to relax your trim/trunc settings a bit to see if that resolves the issue - but with that being said, this error may also occur with really poor read quality as well. If relaxing your trim/trunc settings doesn't resolve the issue, you can also proceed by just using your forward or reverse reads.

Hope this helps!