I have ITS2 region sequenced amplicon sequence data can anyone tell me what is the coordinate for the start and end of the following command which is used for the v4 region in mothur SOP currently I’m working on the study of fungi taxonomy so there coordinates need to change.
pcr.seqs(fasta=silva.bacteria.fasta, start=11895, end=25318, keepdots=F)
I would suggest you follow the instructions on the Mothur webpage to find the coordinates within your database (i.e. SILVA). I followed the instructions because I wanted to find the coordinates for the Acanthamoeba 18S region to do an 18S pipeline, and it worked great! Just make sure you have a good reference microorganism. For example, I downloaded the Acanthamoeba Castellani (which makes sense for my project) 18S region sequence and used the same primers I used for sequencing in this region (just like in the instructions). Then I aligned it with my SILVA database and got the coordinates. This is the link: Customize your reference alignment for your favorite region
This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.