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 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?
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)