I want to conduct picrust2 in Linux.
To do that, I should prepare biom file and fasta file together.
I have tried to obtain FASTA file from table.qza file as below.
but the result is only biom file.
qiime tools export
--input-path Foldername/table.qza
--output-path Foldername/table.FASTA \
How can I revise the qiime2 commend to get FASTA file from qza file ?
If you know any other option to conduct picrust2, plz let me know.
Thank you for your help.
Hello @SingeunOh,
Which command are you trying to run? Are you using the qiime2 plugin for picrust2? It looks like you need the sequences of the ASVs in your analysis. For that you want the FeatureData[Sequence] artifact which is often called rep-seqs.qza or something similar. The feature table in qiime2 does not usually store these sequences.
Thank you colin, I have obtained the FASTA file of the table using rep-seqs.qza file. Besides, I have obtained the biom file from table.qza file using commend below.
qiime tools export
--input-path foldername/representative_sequences.qza
--output-path foldername/reptable.fasta \
qiime tools export
--input-path foldername/table.qza
--output-path foldername/reptable.biom \
Yes, I am trying to picrust2 outside of qiime2 environment.
Thank you for your sincere interests on this.
Hi @SingeunOh
It seems like you have a biom file and are ready to run picrust2.
Are you having additional issues with picrust2?
Thank you for asking me cherman2.
Actually, I'm encountering difficulties in preparing the filtered biom file for my PICRUSt2 analysis. I've come across recommendations for preprocessing steps like removing ASVs present in only one sample or samples with fewer than 30 ASVs. I'm wondering if there are any resources available where someone has already filtered the table for PICRUSt2 preprocessing? Additionally, I'd greatly appreciate it if someone could provide the QIIME2 commands necessary for conducting this filtering. Thank you!
Hello @SingeunOh,
The filtering tutorial will show you how to do that.