# merge sff files

**URL:** <https://forum.mothur.org/t/merge-sff-files/730>\
**Category:** mothur bugs\
**Created:** [December 7, 2011, 9:42am UTC](https://forum.mothur.org/t/merge-sff-files/730 "2011-12-07T09:42:28Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Kirk](https://avatars.discourse-cdn.com/v4/letter/k/f9ae1b/32.png) [@Kirk](https://forum.mothur.org/u/Kirk)\
**Post date:** [December 7, 2011, 9:42am UTC](https://forum.mothur.org/t/merge-sff-files/730/1 "2011-12-07T09:42:28Z")

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hi all,

I have 4 .sff files (each about 250 MB, with a total of about 350000 sequences). When I merge them using the merge.files command, and subsequently subject them to trim.flows(), it just keeps going, with the scrap file-size just increasing with no apparant limit (tens of GB, until I shut down mothur).  
When I process the flow files separately, this works just fine, and quits at the expected sizes.

Any ideas?

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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:** [December 7, 2011, 3:10pm UTC](https://forum.mothur.org/t/merge-sff-files/730/2 "2011-12-07T15:10:39Z")

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Unfortunately, you can’t merge sff files. Especially since you may use the same barcodes in different sff files for different samples. We suggest merging data before running unique.seqs.

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**Author:** ![Kirk](https://avatars.discourse-cdn.com/v4/letter/k/f9ae1b/32.png) [@Kirk](https://forum.mothur.org/u/Kirk)\
**Post date:** [December 7, 2011, 3:16pm UTC](https://forum.mothur.org/t/merge-sff-files/730/3 "2011-12-07T15:16:04Z")

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Yes, I was thinking of doing something like that. Thanks for the advise!

How would you deal with forward and reverse sequences, though? (perhaps not the right forum part)

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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:** [December 7, 2011, 10:09pm UTC](https://forum.mothur.org/t/merge-sff-files/730/4 "2011-12-07T22:09:43Z")

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In that case I’d split the data into a forward pool and a reverse pool and analyze them separately.