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smangul1 / MiCoP

MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.
GNU General Public License v3.0
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Raw read counts #7

Closed mradz19 closed 4 years ago

mradz19 commented 4 years ago

Hi, I am interested in comparing the number of reads assigned to bacteria and fungi in human samples. I have used metaphlan2 for bacterial annotation and I was hoping o use MiCoP for fungal annotation. Does the MiCoP output provide raw sequence counts associated with each taxa or is it just relative abundance values?

nlapier2 commented 4 years ago

Hi,

I've now received multiple requests for an option to output raw read counts instead of relative abundances, so I've now added this feature. Use the --raw_counts option in compute-abundances.py.

Best, Nathan