# Questions on handling genefamilies files

**URL:** <https://forum.biobakery.org/t/questions-on-handling-genefamilies-files/8257>\
**Category:** HUMAnN\
**Created:** [July 15, 2025, 9:18am UTC](https://forum.biobakery.org/t/questions-on-handling-genefamilies-files/8257 "2025-07-15T09:18:06Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![fia](https://avatars.discourse-cdn.com/v4/letter/f/a88e57/32.png) [@fia](https://forum.biobakery.org/u/fia)\
**Post date:** [July 15, 2025, 9:18am UTC](https://forum.biobakery.org/t/questions-on-handling-genefamilies-files/8257/1 "2025-07-15T09:18:06Z")

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Hello, HUMAnN developers:

I have a question regarding the further subgrouping of genefamilies files when the family size is too large. Below is the workflow I followed based on the manual—could you please check if the order is correct?

First, perform humann\_regroup\_table on the genefamilies files obtained for each sample.

Next, apply humann\_renorm\_table to the regrouped genefamilies files for each sample (UNMAPPED are also included in this normalization process).

Then, use humann\_join\_tables on all samples that have been regrouped and renormalized.

Finally, perform humann\_split\_stratified\_table on the file obtained from the third step.

Additionally, I’d like to ask whether the “unmapped” and “ungrouped” rows in the final output can be directly deleted, and whether another round of normalization is needed afterward.

Thank you!

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**Author:** ![franzosa](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/franzosa/32/3511_2.png) [@franzosa](https://forum.biobakery.org/u/franzosa)\
**Post date:** [July 23, 2025, 7:34pm UTC](https://forum.biobakery.org/t/questions-on-handling-genefamilies-files/8257/2 "2025-07-23T19:34:47Z")

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This all sounds reasonable to me!

If you normalize with the “UNMAPPED” and “UNGROUPED” features included, then the resulting abundances reflect the proportions of total read mass in the sample. If you exclude them, then the abundances reflect proportions of the functionally annotated read mass. Both are reasonable things to do / discuss as long as you are clear (more a question of philosophy).

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**Author:** ![fia](https://avatars.discourse-cdn.com/v4/letter/f/a88e57/32.png) [@fia](https://forum.biobakery.org/u/fia)\
**Post date:** [July 24, 2025, 2:50am UTC](https://forum.biobakery.org/t/questions-on-handling-genefamilies-files/8257/3 "2025-07-24T02:50:23Z")

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Thank you for your help!