I am processing paired end V3-4 16S amplicon data sequenced on a MiSeq with a V3 600bp kit. My sequencing data is poor quality and so I would like to run quality-filter q-score on my data prior to cutadapt and Dada2 [note: I know the filtering is redundant to Dada2 and that this is a regularly discussed topic].
Anyways, quality-filter q-score is not processing SampleData[PairedEndSequencesWithQuality] correctly. Everything appears to run as it should -no error messages are thrown- but the output only includes the forward read and reverse reads are discarded. I know this topic is essentially identical to qiime quality-filter q-score does not accept SampleData[PairedEndSequencesWithQuality] but that post is old and from the plugin documentation it appears as though SampleData[PairedEndSequencesWithQuality] is supported.
- Version of QIIME 2: 2021.4 installed in a conda environment
qiime tools import
qiime quality-filter q-score
- Error message?: none, but the output does not produce the expected result based on the plugin information