# Trim silva.bacteria.fasta to V3-V4 region

**URL:** <https://forum.mothur.org/t/trim-silva-bacteria-fasta-to-v3-v4-region/2179>\
**Category:** Theory behind mothur\
**Created:** [December 24, 2014, 5:44am UTC](https://forum.mothur.org/t/trim-silva-bacteria-fasta-to-v3-v4-region/2179 "2014-12-24T05:44:02Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![JingWang](https://avatars.discourse-cdn.com/v4/letter/j/ecb155/32.png) [@JingWang](https://forum.mothur.org/u/JingWang)\
**Post date:** [December 24, 2014, 5:44am UTC](https://forum.mothur.org/t/trim-silva-bacteria-fasta-to-v3-v4-region/2179/1 "2014-12-24T05:44:02Z")

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Hi guys,  
Which start and end point should I use to trim the reference to V3-V4 region? Is there a map table or something?  
I’v tried to use pcr.seqs with V3-V4 primers but failed due to the gaps.  
Or maybe I can remove all the gaps, trim it to V3-V4 region, and align it to something to get the gaps back?  
Thanks.

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**Author:** ![anwesh](https://avatars.discourse-cdn.com/v4/letter/a/ec9cab/32.png) [@anwesh](https://forum.mothur.org/u/anwesh)\
**Post date:** [December 25, 2014, 3:25am UTC](https://forum.mothur.org/t/trim-silva-bacteria-fasta-to-v3-v4-region/2179/2 "2014-12-25T03:25:02Z")

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May be you are looking for this…  
[http://mothur.ltcmp.net/t/pcr-seqs-start-stop-for-v3-5-on-miseq/1608/2](http://mothur.ltcmp.net/t/pcr-seqs-start-stop-for-v3-5-on-miseq/1608/2)

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**Author:** ![JingWang](https://avatars.discourse-cdn.com/v4/letter/j/ecb155/32.png) [@JingWang](https://forum.mothur.org/u/JingWang)\
**Post date:** [December 28, 2014, 5:33am UTC](https://forum.mothur.org/t/trim-silva-bacteria-fasta-to-v3-v4-region/2179/3 "2014-12-28T05:33:30Z")

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> [@anwesh](#):
>
> May be you are looking for this…  
> [http://mothur.ltcmp.net/t/pcr-seqs-start-stop-for-v3-5-on-miseq/1608/2](http://mothur.ltcmp.net/t/pcr-seqs-start-stop-for-v3-5-on-miseq/1608/2)

Thanks, it’s helpful.