Exporting data question

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1

Hi!
It is possiblle change a file .qza to a new file .fasta?
Thanks!

Hi!
It is possiblle change a file .qza to a new file .fasta?
Thanks!

2

Hi!
Do you mean, like this:

mkdir Rep-seqs
qiime tools export \
  --input-path rep_seq.qza \
  --output-path Rep-seqs/
1 Like
3

Ok!
I applied this command and I got a folder called Rep-seqs and inside it two files: sklearn_pipeline.tar and sklearn_version.json.
Some of these files can be converted to .fasta and used to do metagenome taxonomy annotation.
Thanks and best regards!

4

Is it possible convert a qza file to fasta file?
Orcut the regions v3-v4 of database silva 138 .fasta?

5

Hi! Check out this tutorial. You can extract reads by providing primers and obtain a .qza file. This file you can import or open as an archive and extract a fasta file with sequences.

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6

Hi Timur, I was wondering to convert my rep-seq.gz to fast for re-taxon in SILVA web version. The rep-seq.qz already cleaned and flitred. How I can export these data to fasta? Above u said that according to tutorial, we should extract primeres. But why? We alredy had trimmed primres.
Thank you for ur reply in advance.

7

Hi!
As I wrote above, you can use this command to extract a fasta file.

Or open it as an archive, navigate to data directory and extract it to any folder.

You do not need to do it then.

1 Like
8

Thanks, Timur.
Grettings from Moscow)

1 Like
9

Привет Москве :wave:

1 Like
10

Sorry Timur, I aplogise if I am sking so osimple questions. But I am new here, and I need more and more learn. So anyway, I have antoher question. The script, which u mentioned has worked and I got only one fast file. But ideally, I should have got sequences to each sample. Where I was confused, i don;t know. But I must say that, I filttred the rep.seqs.gza from mitochondria and chloroplast, according this script:
#$ -S /bin/bash
#PBS -l walltime=100:00:00
#PBS -d.
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
source /home/shonb/miniconda3/bin/activate qiime2-2020.8
qiime feature-table filter-seqs
–i-data singlendrepresentative_sequences.qza
–i-table table-no-mitochondria-no-chloroplast2.qza
–o-filtered-data lastfiltered-seqs.qza
source /home/shonb/miniconda3/bin/deactivate

11

I am learning here as well

Unfortunately, I am not aware of efficient way to perform it in Qiime2, but maybe someone form Qiime2 team will help you with that.

If you are familiar with scripting in Python or R I would suggest to export your feature table and convert a biom file resulted to .tsv and write a custom script to create multiple fasta files with ASVs for each sample.
But maybe you should annotate it first and then divide it by samples.

12

Hi @ShonB,

the export command is working as expected, returning one sequence file containing all the representative sequences which a re not mitochondria and not chloroplast (assuming the filtering step worked as expected). In this sequence data there is no information indicating which sample contain the sequences, so the best it could do is return them all in the same file.

If you want to get a sequence file for each sample you could work with some scripting as @timanix suggest or try to apply a filtering exporting step for each single sample you need to check, as described in:

Hope it helps
Luca

1 Like
13

Thank you, Luca. I still have been trying to figure out.

14

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