I have filtered the sequences in qza format using deblur
qiime quality-filter q-score
then, how can I convert demux-filtered.qza to fasta?
Your listed command is actually q2-quality-filter (not q2-deblur), but generally speaking you can run:
qiime tools export /filepath/to/artifact.qza --output-dir anything/
to get at the data inside the artifact.
Let me know if that’s what you’re looking for!
Thanks! It works very well!
It works, but I only got three sequences. What is wrong here?
I only got three sequences. Looking forward to your help!
Just to confirm, we are still talking about
It’s possible your filtering parameters are too stringent.
Could you post your
qiime demux summarize output for
import_results.qza as well so we can see what the raw reads looked like?
I think I got a trouble since the first step of imporint data.
I have paired-end sequenceing data (splitted forward and reverse files), and using the following command to import data:
- improting data
qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path data.tsv
example sequencing reads:
the sequencing reads are 244 nt long.
- filtering reads
qiime dada2 denoise-single
- export sequences
qiime feature-table tabulate-seqs
qiime tools export rep-seqs.qzv --output-dir seqout/
But all sequences I got were 120 nt long. What is wrong here?
I think the issue is right here:
You want that to be
qiime dada2 denoise-paired so that your forward and reverse reads are merged.
Right now you are only getting the forward reads back. Which is why they are all
120 bp long, as that was your
Hope that helps!
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