I’ve been following the Schloss SOP and get stuck when I come to the first unique.seqs step as I don’t have a name file to include. Don’t have access to the sff files so jumped straight to trim.seqs. I’ve been using the following code and get the following output.
trim.seqs(fasta=Myfile.fna, oligos=Myfile.txt, qfile=Myfile.qual, maxambig=0, maxhomop=8, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, processors=16)
Output File Names:
Is the name file only generated when using the shhh.flows procedure?
Also, I’ve found that further in the analyses I have issues with names and group files not matching up, don’t know if this is related.
Any help greatly appreciated