Per sample abundances for sub-catalogs

[Matthieu Pichaud]

Hi,

Are the per sample abundance table available for sub-catalogs?

I am interested by GMGC10.human-gut.95nr.fna.gz in particular.

Many thanks for your time considering this question!

Matthieu

[Luis Pedro Coelho]

Hi Matthieu,

Short answer is that we do not provide it. It would have been a massive undertaking to do it properly, but you can get 99% of the result by filtering the original big abundance file (if that makes sense).

Best, Luis

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Luis Pedro Coelho | Queensland University of Technology | https://luispedro.org

https://orcid.org/0000-0002-9280-7885

[Matthieu Pichaud]

It makes perfect sense.
Thank you for the great insight!

[Matthieu Pichaud]

Hi, please allow me this follow-up question.

Would you advise to:

- filter from the big abundance file the counts of the genes in the sub-catalog and dismiss the other counts

or 

- sum (or aggregate somehow) the counts of the genes clustered together in the sub-catalog using GMGC.relationships.txt.gz?

Thanks a lot for your guidance!

[Luis Pedro Coelho]

Filter from the big abundance file. Luis

On Tue, 18 Nov 2025, at 6:01 AM, Matthieu Pichaud wrote:

- filter from the big abundance file the counts of the genes in the sub-catalog and dismiss the other counts

[Matthieu Pichaud]

Hi Luis,

Many thanks for your tome .

I understand why "Filter from the big abundance file" works for the non redundant 100% sub-catalogs,
but for the 95% non redundant, isn't the sum per cluster the right way to go?

[Luis Pedro Coelho]

The abundances were only computed for the 95nr GMGC (what are called unigenes in the manuscript). So sequences that are not present in the nr version don't have an abundance.

The subcatalogs that we provide are subsets of the full catalog (i.e., every sequence in a subcatalog is also present in the big catalog), so the identifiers match.

Best, Luis

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[Matthieu Pichaud]

Awesome.

Thanks for taking the time.