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will-rowe / groot

A resistome profiler for Graphing Resistance Out Of meTagenomes
MIT License
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Abundance table #47

Closed mhmism closed 5 months ago

mhmism commented 3 years ago

Hello,

Thank you for this great pipeline!

Is there a way to merge all groot reports into a single abundance table in a similar way to ASVs/OTUs tables?

Thanks a lot in advance!

will-rowe commented 3 years ago

Hi there. Thanks for your interest in GROOT!

GROOT doesn't have a way to do that built in, but maybe you could do some bash scripting to combine the reports?

If you had an example of what you are after, maybe we could look at adding something to GROOT?

mhmism commented 3 years ago

Thanks will for your kind response.

I will try out some scripting and share once done.

Would it be good to report the read count in this table, or should we consider normalization (e.g. relative abundance, others) before downstream analyses (e.g. differential abundance, diversity, etc.)?

I was thinking something like (read counts are reported), let me know your opinion?

ARG Sample1 Sample2 Sample3 TetQ 150 0 0 mexY 100 0 0 MexZ 0 0 200 mfd 0 19 50