I was thinking it would be nice to be able to view a boxplot showing quality scores across a read after quality filtering (qiime quality-filter) has taken place, as well as immediately after demultiplexing (qiime demux).
This is because I would use the boxplot to choose how to trim my reads before denoising, but currently I can’t visualise how different quality filtering stringency affects the average base quality across the read, and therefore whether filtering would affect my choice of trim length. From the quality-filter stats output, I only know what percentage of reads are retained after quality filtering, not how the removal of those reads would affect the boxplot.
I hope that makes sense! Thanks!
If I am understanding you correctly, you want to be able to generate a
demux summarize plot from data that has been run though
quality-filter? If so, I have good news for you -
demux summarize accepts
SampleData[JoinedSequencesWithQuality | PairedEndSequencesWithQuality | SequencesWithQuality].
quality-filter q-score returns
quality filter q-score-joined returns
SampleData[JoinedSequencesWithQuality], so you should be able to feed either of those back into
If that doesn’t answer your question, can you please provide some additional detail so that I am on the same page as you? Thanks so much!
Hi @thermokarst, that’s exactly what I wanted to do! Thanks so much for explaining!