# \-t marker\_counts output with taxonomy results

**URL:** <https://forum.biobakery.org/t/t-marker-counts-output-with-taxonomy-results/1045>\
**Category:** MetaPhlAn\
**Created:** [September 18, 2020, 3:42pm UTC](https://forum.biobakery.org/t/t-marker-counts-output-with-taxonomy-results/1045 "2020-09-18T15:42:07Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Minjae\_Kim](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/minjae_kim/32/267_2.png) [@Minjae\_Kim](https://forum.biobakery.org/u/Minjae_Kim)\
**Post date:** [September 18, 2020, 3:42pm UTC](https://forum.biobakery.org/t/t-marker-counts-output-with-taxonomy-results/1045/1 "2020-09-18T15:42:08Z")

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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!  
Minjae

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**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [September 24, 2020, 7:44am UTC](https://forum.biobakery.org/t/t-marker-counts-output-with-taxonomy-results/1045/2 "2020-09-24T07:44:18Z")

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

> [@Minjae\_Kim](#):
>
> Also, is it okay to use statistical analysis (e.g., difference-in-difference) with the default output with --unknown\_estimation option?

Yes, I would say so

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<div class="post-metadata">

**Author:** ![Minjae\_Kim](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/minjae_kim/32/267_2.png) [@Minjae\_Kim](https://forum.biobakery.org/u/Minjae_Kim)\
**Post date:** [September 24, 2020, 10:58pm UTC](https://forum.biobakery.org/t/t-marker-counts-output-with-taxonomy-results/1045/3 "2020-09-24T22:58:52Z")

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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!  
Thanks  
Minjae

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<div class="post-metadata">

**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [September 28, 2020, 8:15am UTC](https://forum.biobakery.org/t/t-marker-counts-output-with-taxonomy-results/1045/4 "2020-09-28T08:15:23Z")

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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)