# multiple runs used same barcode
**URL:** https://forum.mothur.org/t/multiple-runs-used-same-barcode/1169
**Category:** Commands in mothur
**Created:** [January 9, 2013, 2:32pm UTC](https://forum.mothur.org/t/multiple-runs-used-same-barcode/1169 "2013-01-09T14:32:50Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@Lxhf](https://forum.mothur.org/u/Lxhf)
#### Post date: [January 9, 2013, 2:32pm UTC](https://forum.mothur.org/t/multiple-runs-used-same-barcode/1169/1 "2013-01-09T14:32:50Z")
Hi,
I first got about 120 .sff files from the company, which did the 454 analysis for us. :shock:
In the end we managed to merge them into 2 separate sff-file, but not one.
This is because they re-used the same bar-codes on two separate runs without any concern on how we designed the experiments. 🕶
I would like to follow the SOP, but I have some doubts how this segregation will effect the shhh.flows command etc.
If anyone has encountered a similar problem, I would really appreciate any suggestion how to handle it.
🙂
Thank you
Alex
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [January 9, 2013, 4:58pm UTC](https://forum.mothur.org/t/multiple-runs-used-same-barcode/1169/2 "2013-01-09T16:58:12Z")
If you want to keep the 2 runs separate, you should create a second oligos file. Then you can use the sff.multiple command, [http://www.mothur.org/wiki/Sff.multiple](http://www.mothur.org/wiki/Sff.multiple), to run trim.flows, shhh.flows and trim.seqs. Something like:
forward CCGTCAATTCMTTTRAGT
barcode AATGGTAC F003D000\_1
barcode AACCTGGC F003D002\_1
barcode TTCGTGGC F003D004\_1
barcode TTCTTGAC F003D006\_1
barcode TTCGCGAC F003D008\_1
barcode TCCAGAAC F003D142\_1
barcode AAGGCCTC F003D144\_1
barcode TGACCGTC F003D146\_1
barcode AGGTTGTC F003D148\_1
barcode TGGTGAAC F003D150\_1
barcode AACCGTGTC MOCK.GQY1XT001\_1
and
forward CCGTCAATTCMTTTRAGT
barcode AATGGTAC F003D000\_2
barcode AACCTGGC F003D002\_2
barcode TTCGTGGC F003D004\_2
barcode TTCTTGAC F003D006\_2
barcode TTCGCGAC F003D008\_2
barcode TCCAGAAC F003D142\_2
barcode AAGGCCTC F003D144\_2
barcode TGACCGTC F003D146\_2
barcode AGGTTGTC F003D148\_2
barcode TGGTGAAC F003D150\_2
barcode AACCGTGTC MOCK.GQY1XT001\_2
You can create a design file, or use the get.groups and merge.groups commands if you would like to pool sequences from the same barcode and different runs later in your analysis.
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### Author:  [@Kendra](https://forum.mothur.org/u/Kendra)
#### Post date: [January 9, 2013, 8:08pm UTC](https://forum.mothur.org/t/multiple-runs-used-same-barcode/1169/3 "2013-01-09T20:08:53Z")
or run the pipeline up through trim.seqs on each file individually then concatenate the fasta, names, and groups files