How are the sequences in qza exported to fasta format?

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1

I have filtered the sequences in qza format using deblur
qiime quality-filter q-score
–i-demux import_results.qza
–o-filtered-sequences demux-filtered.qza
–o-filter-stats demux-filter-stats.qza

then, how can I convert demux-filtered.qza to fasta?

thakns!

3

Hey @hzh0005,

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!

2 Likes
5

Thanks! It works very well!

6

It works, but I only got three sequences. What is wrong here?

7

I only got three sequences. Looking forward to your help!

9

Just to confirm, we are still talking about demux-filtered.qza right?

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?

Thanks!

11

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:

  1. improting data
    qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path data.tsv
    –output-path import_results.qza
    –source-format PairedEndFastqManifestPhred33

example sequencing reads:
@M04650:146:000000000-BJ6B3:1:1101:16660:1969 1:N:0:8
ACTCCTACGGGAGGCAGCAGTGGGGAATCTTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAGCGATGAAGCCCTTCGGGGTGTAAAGCTCTTTCGACGGGAACGATAATGACGGTACCCGGAGAATAAGCTTCGGCTAACTACGTGCCAGCAGCCGCGGTATTACGTAGGCAGCGAGCGTTGTTCGGTGTTACTGGGCGTAAAGGTTGTGTAGGCGGTTCTCTTTGTTTGGTGTG
+
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG>EDFGEFF88F,@9@E:+++@F+@4C+,4+B=A9?E=DFGG7+++@:FAA<,?BFGGGG++3+=++3B7+>7:F99=++FC+8,++,3,8D,8>><,3?,?>F8<<A,684CC7C7,?*4,27<78*:C*;C9*2;?+<F++/2*0++0;/A9+++2:8:+2+++3;:C:5:

the sequencing reads are 244 nt long.

  1. filtering reads

qiime dada2 denoise-single
–p-trim-left 0
–p-trunc-len 120
–i-demultiplexed-seqs …/import_results.qza
–o-representative-sequences rep-seqs.qza
–o-table table.qza

  1. export sequences
    qiime feature-table tabulate-seqs
    –i-data rep-seqs.qza
    –o-visualization rep-seqs.qzv

qiime tools export rep-seqs.qzv --output-dir seqout/

But all sequences I got were 120 nt long. What is wrong here?

13

Hi @hzh0005,

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 --p-trunc-len.

Hope that helps!

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