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.