Adding taxonomy information when constructing the refpkg

[Adi Lavy]

Hi all!

This question is more about using taxtastic but I could not find where to ask it other than here, so I apologize upfront if this might not be the proper place.

In any case, here is my question:

I am trying to make a refpkg for non 16S rRNA database which will include taxonomy information. I understand the part that downloads the latest NCBI db using the command : 

taxit new_database -d taxonomy.db

However, I do not understand how to generate the tax_id.txt file needed in order to pull the taxonomy that is relevant to my project, and how the taxonomy information will be linked to the actual sequences that are in my database.

I've found the following example:

taxit taxtable -d taxonomy.db -t tax_id.txt -o taxonomy.csv

where tax_id.txt would probably hold this information, but what should be the table structure? Could someone please provide an example?

Thank you!

Adi

[Noah Hoffman]

Hi Adi,

Ultimately, the mapping of reference sequences included in the refpkg
to tax_ids is provided by the "seq_info" file (see
http://fhcrc.github.io/taxtastic/refpkg.html). You can use this file
to specify tax_ids to include in the taxonomy information produced by
'taxit taxtable' using the -i/--seq-info option:

taxit taxtable -d taxonomy.db -i seq_info.csv -o taxonomy.csv

Hope that helps,
Noah

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