# HumanN: which reference database? why so many ummaped reads? **URL:** \ **Category:** HUMAnN\ **Created:** [June 25, 2021, 11:47am UTC](https://forum.biobakery.org/t/humann-which-reference-database-why-so-many-ummaped-reads/2298 "2021-06-25T11:47:04Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![luciagg](https://avatars.discourse-cdn.com/v4/letter/l/b5a626/32.png) [@luciagg](https://forum.biobakery.org/u/luciagg)\ **Post date:** [June 25, 2021, 11:47am UTC](https://forum.biobakery.org/t/humann-which-reference-database-why-so-many-ummaped-reads/2298/1 "2021-06-25T11:47:04Z")
Hello everyone, I’m getting into the use of HumanN and as I understand, HumanN can be used with different reference databases: Unifref90, Uniref50, KEGG. I would like to ask, which one is more recommended? Until now, I have tried this commands: _humann2\_databases --download chocophlan full /home/noe/Desktop/Shotgun\_Lucia/humann2database/chocophlan_ \*parallel -j 1 ‘humann2 --metaphlan-options “–bt2\_ps very-sensitive-local --min\_alignment\_len 50” --eta --threads 12 --input {} --output humann2\_out/{/.} --memory-use maximum’ ::: _fast_q And obtained a very high proportion of unmapped reads (68%), I attached the results. [humann2\_pathabundance\_relab\_unstratified.txt](https://forum.biobakery.org/uploads/short-url/ka7q3TNcjB4GIYk7BHAyCm2TT5o.txt) (15.0 KB) Is it normal or could it be due to an inappropriate reference database? Thanks you in advance, Lucia ---
**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 6, 2021, 5:37pm UTC](https://forum.biobakery.org/t/humann-which-reference-database-why-so-many-ummaped-reads/2298/2 "2021-07-06T17:37:36Z")
I recommend UniRef90 for human-associated communities (or anything else that is comparably well studied) and UniRef50 for everything else.