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
-commands:
qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path 16S_manifest.tsv
–output-path demux.qza
–input-format PairedEndFastqManifestPhred33V2
qiime quality-filter q-score
–i-demux demux.qza
–p-min-quality 12
–p-quality-window 3
–p-min-length-fraction 0.83
–o-filtered-sequences demux_qfilter.qza
–o-filter-stats stats_qfilter.qza
- Error message?: none, but the output does not produce the expected result based on the plugin information