shhh.flows and editing results

I have a bit of a problem. I sequenced 31 samples and in the first run one of the samples had problems. We resubmitted the sample and the sequencing centre ran it on another plate for us (no problem the second time around).

The problem is that they used a barcode for the second run that was already used for a sample in the first run. I have two sff files and I’m not quite sure what to do. I can’t find any info on editing raw sff files. Can I legitimately run shh.flows on both of these and then concatenate the resulting .fasta and .names files after running trim.seqs? Or should I just go with trim.seqs and the fasta and qual files that were supplied?


Hi Bob,

I’d process the first 30 samples through trim.flows, shhh.flows, and trim.seqs. Then I’d process the extra sample through the same steps. Finally, I’d merge the two *.trim.fasta, *groups, and *names files and go on your merry way…