# Repeat sub.sample command

**URL:** <https://forum.mothur.org/t/repeat-sub-sample-command/2828>\
**Category:** Commands in mothur\
**Created:** [April 27, 2016, 6:29am UTC](https://forum.mothur.org/t/repeat-sub-sample-command/2828 "2016-04-27T06:29:31Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![ghaida\_ali](https://avatars.discourse-cdn.com/v4/letter/g/aeb1de/32.png) [@ghaida\_ali](https://forum.mothur.org/u/ghaida_ali)\
**Post date:** [April 27, 2016, 6:29am UTC](https://forum.mothur.org/t/repeat-sub-sample-command/2828/1 "2016-04-27T06:29:31Z")

</div>

Hi,

I would like to ask if it possible to run the subsampling command for couple of times, not just once. It been suggested to me to make sure that I got all the sequences after running this command, instead of getting rid of the important sequence that i could get.

Can you please clarify to me this point if is it possible and why in case of no ?

  
Thanks

Best,  
Ghaida

---

<div class="post-metadata">

**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [April 28, 2016, 11:18am UTC](https://forum.mothur.org/t/repeat-sub-sample-command/2828/2 "2016-04-28T11:18:29Z")

</div>

You can rarefy the data in summary.single and dist.seqs by using subsample=T or subsample=### where ### is the number of sequences you want. This will subsample 100 or 1000 times and then give the average. The sub.sample command can be run multiple times on a shared file, but it will write over the results each time. This is really only appropriate when you’re investigating the associations for individual OTUs.

Pat