We are using the Staden package (primarily pregap) to "clean-up" sequences
prior to placing them in a blast searchable database. All of the data is
collected on ABI sequencers, however some of the files seem to be improperly
parsed by pregap, and these same files are not visible using the version of
ted that we are using.
This behavior seems to correlate with the instrument on which the files were
collected, with those collected on a 373 not visible whereas those collected
on a 377 *do* work. We suspect there is a difference in the file formats
between the two, but the person I talked to at ABI said that their file
formats were proprietary.
I found a Staden FAQ news thread where people were talking about different
file formats and their compatibility with the Staden programs, but they were
all quite out of date.
Does anyone know about this phenomenon? I just subscribed to this newsgroup,
so if everybody is sick to death of answering this question, can anyone point
me to some documentation on the issue? Will I have to suuport two versions
of all the Staden programs until such a time as we upgrade to the latest ABI
software on all the machines?
Thanks for your trouble!
(PS we are collecting data on a Macintosh, then transferring the data in
MacBinary mode to a sparc station)
DNAX Research Institute