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motu-tool / mOTUs

motus - a tool for marker gene-based OTU (mOTU) profiling
GNU General Public License v3.0
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Count table output? #117

Closed ayabrown closed 9 months ago

ayabrown commented 10 months ago

Hi, I was wondering why the '-c' option (or similar) for count table is no longer available in v3.0.

I was able to get the intermediate count table (of each MG) in v3.0 when running with '-M' option but not a per-taxa one.

any help would be much appreciated,

Aya

hjruscheweyh commented 10 months ago

Hello @ayabrown

The -c option is still part of the mOTUs pipeline. When running profile with -M you will also create the MGC file which also produces the markergenecluster abundances (not the taxa, but of individual markegeneclusters inside a taxa). This MGC file is only an intermediate file that is produced to avoid re-parsing of big BAM files. The mOTUs file (-o) should have the abundances as counts when you specify the -c parameter.

Best, hans

ayabrown commented 10 months ago

got it! Thank you so much!