# Merging datasets (miseq)

**URL:** <https://forum.mothur.org/t/merging-datasets-miseq/2212>\
**Category:** Commands in mothur\
**Created:** [January 22, 2015, 9:58am UTC](https://forum.mothur.org/t/merging-datasets-miseq/2212 "2015-01-22T09:58:22Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Somebodyatthedoor](https://avatars.discourse-cdn.com/v4/letter/s/a3d4f5/32.png) [@Somebodyatthedoor](https://forum.mothur.org/u/Somebodyatthedoor)\
**Post date:** [January 22, 2015, 9:58am UTC](https://forum.mothur.org/t/merging-datasets-miseq/2212/1 "2015-01-22T09:58:22Z")

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Hi,

I currently have two datasets from two sequencing runs which have both been put separately through the Miseq SOP up till classify.seqs. I am now wanting to compare some of the samples from one run to some of the samples from the other.

I am presuming that to do this I will have to somehow extract the samples I’m interested in and merge them into one file. I also thought I would have to redo some of the commands so that similar sequences from the two runs would be clustered together properly.

However, I’m not completely sure which files I should be merging together to do this. Would combining the fasta files from just before preclusterring be the best idea? I’m also not completely sure which commands I would have to use for extracting/merging sequences and whether I would also have to merge anything other than the fasta files (count files etc.).

Can anyone help?

Thanks,

Laura

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**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:** [January 23, 2015, 6:17pm UTC](https://forum.mothur.org/t/merging-datasets-miseq/2212/2 "2015-01-23T18:17:00Z")

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You’ll likely want to go back to your files file and start again. You can merge the files file and just proceed as you did before.

Pat