# remove primers and update groups file

**URL:** <https://forum.mothur.org/t/remove-primers-and-update-groups-file/3246>\
**Category:** mothur bugs\
**Created:** [May 8, 2017, 9:21pm UTC](https://forum.mothur.org/t/remove-primers-and-update-groups-file/3246 "2017-05-08T21:21:02Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![spaver](https://avatars.discourse-cdn.com/v4/letter/s/a183cd/32.png) [@spaver](https://forum.mothur.org/u/spaver)\
**Post date:** [May 8, 2017, 9:21pm UTC](https://forum.mothur.org/t/remove-primers-and-update-groups-file/3246/1 "2017-05-08T21:21:02Z")

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My raw data consists of illumina reads in fastq files that are separated by sample but the primers have not been removed. Is there a route for analyzing these sequences in mothur?

I have tried make.contigs and trim.seqs, but:

- since I do not have barcodes to remove, I cannot figure out how to get make.contigs to remove primer sequences.
- I tried using trim.seqs to remove primer sequences, but that route did not update the groups file to reflect sequences removed because they did not have the primer sequences. This became a problem at the count.seqs step in the miseq sop workflow, which generated the following error:

[ERROR]: processes reported processing 22973793 sequences, but group file indicates you have 23525510 sequences. Either you have a file mismatch or a process failed to complete the task assigned to it.

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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:** [May 11, 2017, 12:09pm UTC](https://forum.mothur.org/t/remove-primers-and-update-groups-file/3246/2 "2017-05-11T12:09:48Z")

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You can remove primers in make.contigs with an oligos file. You can also use trim.seqs if you give it the oligos file and the group file from make.contigs.

Pat