The bioBakery help forum

-t marker_counts output with taxonomy results

Hello, metaphlan3 team
I’m trying to use -t marker_counts option to use DESeq2 for the normalization but it seems we cannot get the results with taxonomic information.
Is there a source for compiling the genes into taxonomy information with -t marker_counts output?
Also, is it okay to use statistical analysis (e.g., difference-in-difference) with the default output with --unknown_estimation option?
Thanks in advance!

marker_counts reports only the maker ID, you can get the taxonomy associated to the marker from the pkl file

Yes, I would say so

Thanks for the reply!
From the mpa_v30_CHOCOPhlAn_201901_marker_info.txt file, Can I use the taxon element as the key for the python dictionary for combining multiple marker genes into one?
For example, If I have counts for two marker gene IDs that have the same taxon element, I can sum these two value and merge into that taxon.
Please let me know!

No, since quasi-markers are not taken into consideration for the relative abundance calculation since they are not 100% unique to the species. If you are interested in knowing the estimated number of reads mapping against each profiles species, you can run MetaPhlAn with the -t rel_ab_w_read_stats option (estimated_number_of_reads_from_the_clade column of the output)