sff break

Hi - is it possible to break a sff file
into separate sff files according to
the different barcodes used?
Thanks for comments on this.

You can parse a sff file into separate sff files for each sample by running the sffinfo command with an oligos file, http://www.mothur.org/wiki/Sffinfo#oligos.

Thanks - but when I try sffinfo on a barcode sorted sff file,
I get this warning “your sff file may be corrupted… Clip qual right…”
The “opened” files are empty or nearly empty. Can I please have
some comments on this as well?

What version of mothur are you using? Does it process the sff file without the oligos file?

Version v.1.30.1. Sffinfo seems fine withouth the oligo file.
Updated to v.1.31.2 (32 bit Windows), I am afraid I got the same
warning. Thanks for the reply.

Could you send your sff and oligos file to mothur.bugs@gmail.com?

I was able to confirm the problem. It appears to be only an issue with the Windows version of mothur. I haven’t resolved it yet, but in the meantime as a workaround you could try it on a mac or unix/linux machine.

This will be resolved in version 1.33.0.