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eggnogdb / eggnog-mapper

Fast genome-wide functional annotation through orthology assignment
http://eggnog-mapper.embl.de
GNU Affero General Public License v3.0
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does eggnogMapper gives gene abundance #314

Closed khemlalnirmalkar closed 3 years ago

khemlalnirmalkar commented 3 years ago

Hi, Does eggnogMapper give gene abundance/KO/pathways abundance values?

Thanks,

Cantalapiedra commented 3 years ago

Hi @khemlalnirmalkar ,

no abundances are reported in eggNOG-mapper. Do you mean as a summary of terms found in the annotations or as counts from mappings reads to genes or anything else?

Best, Carlos

khemlalnirmalkar commented 3 years ago

Hi @Cantalapiedra , I want to know the difference of genes or pathways between my study groups. So, I am looking for the best way to report that. Does eggnogMapper, give counts from mappings reads to genes? can we quantify genes/KO? Thanks

Cantalapiedra commented 3 years ago

Hi,

eggNOG-mapper is all about functional annotation (guessing what is the function of your genes). For quantification you should use other software. Once you have the counts (normalized counts, for example) you can combine functional annotation + counts to compare your samples.

I hope this makes sense.

Best, Carlos

khemlalnirmalkar commented 3 years ago

yes, completely make sense,

Now i am looking for quantification software, Thanks, Khem

Cantalapiedra commented 3 years ago

You are welcome. Reopen or reissue in case of need. Best, Carlos