I saw there an old post to which replies are no longer allowed, so I figured I would post my own. I’m trying to use dada2 on f and r reads, but I have some sequences that are too short. Here are my demux files.
I’m wondering if there are only a few reads that are too short, and if so - could I remove them to move forward? In the previous post, it was suggested that they use only their forward reads but I was wondering if there was another option.
Some background: My sequences are in the mixed orientation format and I’m re-processing using advice provided here. Previously I had used cutadapt to deal with the mixed orientation issue and dada2 worked fine after that. I assume the short sequences were tossed away in that process… So here is the error I’m getting now
Plugin error from dada2:
No reads passed the filter. trunc_len_f (237) or trunc_len_r (287) may be individually longer than read lengths, or trunc_len_f + trunc_len_r may be shorter than the length of the amplicon + 20 nucleotides (the length of the overlap). Alternatively, other arguments (such as max_ee or trunc_q) may be preventing reads from passing the filter.
Debug info has been saved to /var/folders/gc/t0lly6tx217bq0p81wrgmtp80000gn/T/qiime2-q2cli-err-5xu23z7q.log