V6 region extract from SILVA database

Hello community!!!
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,

are these the sequences you are trying to id to genus? v6 isn’t going to give you that level of resolution very often.

The easiest way to figure this out is to align a few sequences to the full dataset, summary.seqs that to get the start and end number.

1 Like

Thanks for the response.
Yes, these are the sequences i’m trying to identify to genus.
So, are you suggesting to take few subsampled sequences and then do “align.seqs” followed by “summary.seqs”? And at least how many sequences will you suggest for that alignment?

Thanks and regards,

I think I usually do ~100, I just use the head command to get the top X sequences.

1 Like

I saw your PM. The sequences you are working with are 454, so single direction was the way it was done. Single direction reads from 454 were much better than single direction reads in Illumina. Make sure you look at the 454 SOP and run the denoising (pyronoise? I think)

Thanks Dr. Kendra for your valuable suggestion. :slightly_smiling_face:

If you want to generate a V6 specific database, you need to follow the directions at https://mothur.org/blog/2016/Customization-for-your-region/

1 Like

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.