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