'Bacteria' in the result of combined_graphs_unified.R

transcript / samsa2

SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.

GNU General Public License v3.0

54 stars 36 forks source link

'Bacteria' in the result of combined_graphs_unified.R #45

Closed Shicheng-Guo closed 4 years ago

Shicheng-Guo commented 4 years ago

Hi Sam,

Applying combined_graphs_unified.R and SAMSA2 pipeline, I obtained a figure as the blow. My question is how to understand the 'Bacteria' in the Genus list since I think all others also belong to bacteria, right? Hope to receive some explanation to my confusion. Thanks.

Shicheng

SAMSA2-2020-Shicheng-Guo-Strain-Skin

transcript commented 4 years ago

Hi Shicheng,

You're correct - the Bacteria entry is for annotations that are not specific beyond the Bacteria kingdom. There are some entries in the RefSeq database that are just labeled as "bacterial spp.", without any more detailed taxonomic information. These ones are classified here as this Bacteria top-level category.

Shicheng-Guo commented 4 years ago

Dear Sam,

So here should I take the value as 'overall bacteria' reads or "unclassified bacteria" reads?

Thanks.

Shicheng

transcript commented 4 years ago

Hi @Shicheng-Guo,

This would be "unclassified bacteria" reads.

Best, Sam