Extract 16S rRNA V6 region
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18 months ago
dpc ▴ 210

Hi there!!!

I want to find gut microbiome composition from V6 region of 16S rRNA sequence. Unidirectional sequencing was done with 917F & 1391R primers. I am using MOTHUR software. Can anybody please tell me how can I extract the V6 region from the SILVA database using pcr.seqs command?

For V3-V4 region we can use the command: pcr.seqs(fasta=silva.bacteria.fasta, start=6388, end=25319, keepdots=F,processors=8)

Similarly, what start and end position can we use for V6 region?

Thanks and Regards

16S rRNA MOTHUR taxonomy microbiome • 581 views
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Read this: https://mothur.org/blog/2016/Customization-for-your-region/

Follow same for getting start and end position for V6 region

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Thanks a lot gayachit.

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