Hey there)
I am new in QIIME2 and often confused in some analyses.
Anyway, I am trying to get separate sequences (already filtered from any chloroplast, mitochondria and etc.) from rep.seqs.gza for further making fingerprints in SILVA web version. But after filtering and exporting I got only one fast file, where I think all sequences are included.
And I was wondering, how I can get .tar or .fasta files which are divided by samples?
I don’t need to obtain table files, I need procecced sequences of each samples.
Thank you in advance.
Hi @ShonB,
please look at:
It looks as you need to create a filtered abundant table for each of your sample, and use this to filter the sequences from the no-mitochondria and no-chloroplast sequence file.
hope it helps
Luca
PS thank you very much for opening a new thread with this question!
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Could you refer to possible commands we could use? As a representative sequence file has been generated, what do we need to get that exported as FASTA categorised by group. I have tried the feature-table command, however the file is exported in BIOM format. Thanks in advance.
Hi @SafiraLoebis, welcome in the forum!
I think th eeasy way to do what you asking is by using:
https://docs.qiime2.org/2021.2/plugins/available/feature-table/filter-seqs/
You will need the full feature-table and rep-seq data, you can specify the group you need by using the ‘–p-where’ option and specifying the full metadata file with the ‘–m-metadata-file’ option.
Let us know how it goes
Luca
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