Hi @thermokarst, thanks for your reply.
My understanding is that there should be a reverse read for each forward read, so shouldn’t forward and reverse reads have the same number anyway? (though number of unique sequences may be different). I’m still starting out in this research space, so apologies if I’m mistaken.
If I view the fastq files, the forward and reverse reads do not appear identical.
That said, I have located some clues as to why there is an error. A similar problem was reported previously on the qiime2 forums, and the cause appeared to be related to issues with merging/joining forward and reverse reads (Qiime dada2 denoise-paired end sequences). When I attempted to join the reads in the problematic run using another utility (fastq-join from ea-utils), the “success rate” was much lower than what I see in other runs (<0.1%). So it may be a problem with the actual data, although I’m still at a loss as to what exactly is wrong with it. As far as I could tell, primer sequences were removed prior to analysis.
I will continue looking into this
- H