Question: Extract 16S rRNA V6 region
0
gravatar for dpc
5 months ago by
dpc140
India
dpc140 wrote:

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

ADD COMMENTlink modified 5 months ago • written 5 months ago by dpc140

Read this: https://mothur.org/blog/2016/Customization-for-your-region/

Follow same for getting start and end position for V6 region

ADD REPLYlink written 5 months ago by gayachit200

Thanks a lot gayachit.

ADD REPLYlink written 5 months ago by dpc140
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