Groups file - trivial question

Commands in mothur
1

Hi,

This is a very trivial question. But when you run;

trim.flows
shhh.flows
trim.seqs

…the groups file is generated in the second step (shhh.flows), but the e.g. fasta file continues being edited (removing homopolymers etc in trim.seqs) so in forthcoming steps (e.g. in screen.seqs), the groups file will not correspond exactly to the e.g. fasta file…?

Thanks,

2

Yeah this is a bit screwy, but when you run trim.seqs you remove the primers and barcodes and create a new groups file that will correspond to the other outputs from trim.seqs.

3

Great! Thanks!