Rescript: to Generate Functional Genes' Taxonomy and Sequence References

[TurboQiimer]

Hi all,
I am trying to retrieve sequence and taxonomy references for special functional gene (not 16S gene). In this page below it is redirected me to Blast page, but I do not know how to provide first my desired refseq by Blast. The page is empty, no option to pick it up. And I do not have any file to upload.
https://www.ncbi.nlm.nih.gov/refseq/targetedloci/

The desired organism is bacteria. I follow this page again:
https://www.ncbi.nlm.nih.gov/refseq/targetedloci/

By the way, in this command there is an example to extract taxonomy, but one option ('33175[BioProject] OR 33317[BioProject]') is unclear to me! How to provide this? I do not understand what it is.

qiime rescript get-ncbi-data \
    --p-query '33175[BioProject] OR 33317[BioProject]' \
    --o-sequences ncbi-refseqs-unfiltered.qza \
    --o-taxonomy ncbi-refseqs-taxonomy-unfiltered.qza

Using RESCRIPt to compile sequence databases and taxonomy classifiers from NCBI Genbank

This tutorial will describe how to create custom reference databases from NCBI Genbank using RESCRIPt. Read more about RESCRIPt here: https://forum.qiime2.org/t/processing-filtering-and-evaluating-reference-sequence-data-with-rescript/15494/7 If using NCBI Genbank data, please be aware of the NCBI disclaimer and copyright notice. Citation: If you use RESCRIPt or any RESCRIPt-processed data in your research, please cite the following pre-print: Michael S Robeson II, Devon R O'Rourke, Benjami…

Can I use --p-n-jobs parameter in this command and other commands in this case? There is no special page for docstring and tutorial for reecript like other available plugins are installed in default for Qiime2. It is confusing.

I am looking forward to hearing from you.
Thanks a lot.
Qiimer

[Nicholas_Bokulich]

@TurboQiimer

I do not know how to provide first my desired refseq by Blast.

The tutorial that you linked to provides information on the "query" option, and most importantly links to the NCBI documentation, which describes entrez queries in more detail. This option takes an entrez query (or list of Genbank sequence IDs) and you must refer to the entrez documentation to learn how to create a proper query, if you want to use that option.

@TurboQiimer

one option ( ‘33175[BioProject] OR 33317[BioProject]’ ) is unclear to me! How to provide this? I do not understand what it is.

Did you read the tutorial that you linked to? It describes how to use the "query" option. In this case, the query is pulling data from two specific "bioprojects" (the 16S refseq data)... but any valid entrez query can be used.

@TurboQiimer

Can I use --p-n-jobs parameter in this command and other commands in this case? There is no special page for docstring and tutorial for reecript like other available plugins are installed in default for Qiime2. It is confusing.

This is not a "core" QIIME 2 plugin so is not listed on the "available plugins" page at qiime2.org, and is not installed by default. As with all other QIIME 2 commands, though, you can type the action name plus "--help" to see the help documentation.

Good luck!