I am working with MiSeq data. However, each sequence has between 1 and 10 random bases prior to the beginning of the 16S forward read, due to the type of amplification I did. I would love to be able to have each sequence start exactly at the beginning of the 16S primer (or end of the primer), so when I use unique.seqs, I actually get them. Any current commands in mothur that can do this for me? Any other suggestions? Thanks!
You could try doing something like…
NCCTACGGGAGGCAGCAG
NNCCTACGGGAGGCAGCAG
NNCCTACGGGAGGCAGCAG
NNNCCTACGGGAGGCAGCAG
etc.
I ended up just using a wildcard find and replace in my text editor.
That works too!