I am analyzing Miseq data at first time using Mothur. Looks clear at the beginning. But stuck in the step of aligning. How do I know the point where in the alignment my sequences start and end.
Can you take a 16S sequence (say from E. coli) and trim it to the region amplified by your primers? Then align that sequence against silva.bacteria.fasta. Then run the output of that through summary.seqs. That will give you the start and end coordinates to use to get your region of interest.