make.sra on 454 data

I am trying to submit the sequences from my project to the SRA database and I wish to use the make.sra command to prepare the submission.
My problem is the following: for my study I used one whole 454 sequencing plate and an additional half-plate, sharing the “space” with someone else. Thus, my second sequencing plate contains groups from two projects and I just want to submit the sequences for one of them. I just have one sff file but I do not want to use it all… how can I remove the groups that I do not want to submit yet, and get another sff file to use with the make.sra command?
Thank you!!

Here’s what I would recommend.

mothur >, oligos=yourOligosFile, pdiffs=2, bdiffs=1) - creates a sff file for each sample mothur > make.sra(file=fileContaingingParsedSFFYouWant, ....)
The fileContaingingParsedSFFYouWant should look like:

sffFileForSample1 oligosFile
sffFileForSample2 oligosFile
sffFileForSample3 oligosFile
sffFileForSample4 oligosFile