I have a 454 study using a different (i.e. non-16S) gene, and was wondering exactly what changes should I make to the Schloss SOP.
I’m guessing this will involve the creation of custom databases…
Yeah, you’d have to come up with a reference alignment and taxonomy database. Other than that you should be good to go…
I also have a 454 study using a different gene. In my case, I have 18S rRNA sequences that I was able to process using the Schloss pipeline (designed for 16S) up to the point where I removed chimeras. After that, I want to classify my sequences using the online taxonomic classification available in silva (http://www.arb-silva.de/aligner/)
If I obtain a fasta file with the classified sequences, can I go back to mothur and continue using the pipeline I was using before? I wonder, for example, if I need to create a new name file? (not sure)
Any comment or suggestion would be highly appreciated.