# Problem with oligos file in trim.flows
**URL:** https://forum.mothur.org/t/problem-with-oligos-file-in-trim-flows/2787
**Category:** Commands in mothur
**Created:** [March 25, 2016, 11:15pm UTC](https://forum.mothur.org/t/problem-with-oligos-file-in-trim-flows/2787 "2016-03-25T23:15:33Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@hmvantol](https://forum.mothur.org/u/hmvantol)
#### Post date: [March 25, 2016, 11:15pm UTC](https://forum.mothur.org/t/problem-with-oligos-file-in-trim-flows/2787/1 "2016-03-25T23:15:33Z")
Hello! This is my first time using mothur. Thanks in advance for any help!
I want to analyze published data from [http://www.ncbi.nlm.nih.gov/sra?term=SRR770064](http://www.ncbi.nlm.nih.gov/sra?term=SRR770064). I’m using the 454 SOP but running into problems at the trim.flows step - everything winds up in my SRR770064.scrap.flow file. I suspect this has something to do with my oligos file because I get some content in my SRR770064.trim.flow file if I remove the oligos option. Or maybe it has something to do with the other options I chose in the trim.flows command?
Here is my oligos file (there are no barcodes):
```nohighlight
forward TTGACGGGGGCCCGCACAAG
#reverse TACCTTGTTACGACTT
```
This puts everything in the SRR770064.scrap.flow file:
```nohighlight
trim.flows(flow=SRR770064.flow, oligos=SisonMangus2014.oligos, pdiffs=2, processors=2, minflows=450, maxflows=450, order=A)
```
This works, but don’t I need the oligos file for something?
```nohighlight
trim.flows(flow=SRR770064.flow, processors=2, minflows=450, maxflows=450, order=A)
```
---
### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [March 29, 2016, 11:55am UTC](https://forum.mothur.org/t/problem-with-oligos-file-in-trim-flows/2787/2 "2016-03-29T11:55:36Z")
I suspect you’re missing the barcode in your oligos file. These are not removed from the sff files and precede the primer.
Pat
---
### Author:  [@hmvantol](https://forum.mothur.org/u/hmvantol)
#### Post date: [March 29, 2016, 8:49pm UTC](https://forum.mothur.org/t/problem-with-oligos-file-in-trim-flows/2787/3 "2016-03-29T20:49:19Z")
There are no barcodes in this data. Each sequence starts with the forward primer. Does the function not like that it can’t find any?
---
### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [April 1, 2016, 12:56pm UTC](https://forum.mothur.org/t/problem-with-oligos-file-in-trim-flows/2787/4 "2016-04-01T12:56:02Z")
Taking one of the sequences from the SRA site (see the reads tab at [http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR770064](http://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR770064)). You get something like this…
```nohighlight
>gnl|SRA|SRR770064.8 GSVBTXW01A46MC
tcagAGAGATGTTTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGC
AACGCGAAGAACCTTACCAGGGTTTGACATGATACGAATTTCTTTGAAAGAAGAAAGTGC
CTTTTGGAACGTATACACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTG
GGTTAAGTCCCGCAACGAGCGCAACCCTTATTTTTAGTTGCCTATTTGGAACTCTAGAAA
GACTGCTGGTTATAAACCGGAGGAAGGCGGGGATGACGTCAAGTCAGCATGCCCCTTACA
CCCTGGGCTACACACGTGCTACAATGGGTGAGACAATGAGATGCAAATCTGCGAAGACAA
GCTAATCTATAAACTCTCTCTAAGTTCGGATTGTAGGCTGCAACTCGCCTGCATGAAGTT
GGAATCGCTAGTAATCGCTGGTCAGCTATACAGCGGTGAATTCGTTCCCGGGCTTGTACA
CACCGCCCGTCACACCATGGAAGCTGGTTANCGTACGNNN
```
The ‘tcag’ is the control tag. You’ll see that your primer (TTGACGGGGGCCCGCACAAG) is 8 bases into the sequence and that it actually has a barcode - AGAGATGT. This is why it’s scrapping everything.
Pat
---
### Author:  [@hmvantol](https://forum.mothur.org/u/hmvantol)
#### Post date: [April 1, 2016, 9:14pm UTC](https://forum.mothur.org/t/problem-with-oligos-file-in-trim-flows/2787/5 "2016-04-01T21:14:21Z")
Oh I see! Thanks a lot!