But why is it showing up in step3's output as a read, if I did grep all of the directories and it doesn't show up in any of them? Sincerely yours, Robin On Wed, Mar 23, 2011 at 6:38 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote: > On Thursday 24 March 2011 01:33:32 Robin Kramer wrote: > > > That is what I thought, but I can't seem to find much assembly > information > > > for this particular read in step2. It is in the step2_reads.caf file, but > > > there are no reads associated with it, to go back to step1. I was > > > expecting it to be in the step2_strainname directory, but it isn't in any > > > of the caf, fasta, or various info files either. > > "rgrep" is your friend :-) > > If that read is not in any of the "step2_*" directories (don't forget the > 'default' "strainname"), it has been dropped after step1. > > B. > >