Provision of DNA Sequencing as a core facility

Ian Ian
Fri May 16 07:59:40 EST 1997


>        At the moment, I am experiencing some bizarre problems, which I think
>relate to networking : In essence, the collection software is mixing up
>samples when new sample files are being generated after manual tracking
>of a gel.

When the gel is initially "automatically" tracked sample files and .seq
files are generated, if you then manually track you would expect the old
ones to be overwritten by the new, this is generally the case.

BUT if (old) sample and .seq  files have been generated and then you
retrack the gel, and then any of the lanes are either empty or failed then
a new .seq file will not be created and so you end up with a new sample
file but still the old .seq file.

To avoid this I always remove all samples from the sample manager and all
the files from the run folder before I retrack and extract.

Hope that all made sense!!!!

>In addition, the gel file is jamming and during manual
>tracking etc

The gel jams occasionally for me when I've moved a gel image to the other
computer, closing the gel file and then reopening seems to sort this out,
but obviously it's not ideal.

>        I would like some specific answers on the following questions :
>1. Should I shut down file sharing, period ,on the collection mac or
>just during collection itself ?


>2.As a follow on from the above, is it o.k to write sample files over
>the network form the collection mac,or is it preferable to have a second
>mac for disrtibuting data ?

Shouldn't be a problem although I do have a second mac acting as a server.

>3. I have started archiving data to an Iomega jaz drive, although I Am
>led to believe that these drives in the context of sequence analysis
>data may cause problems. Is there any truth in this ? Incidentally, when
>I first tried to install the driver software onto the collection mac it
>wouldn't have it and subsequently one of the apple talk extensions
>became jammed. Ever since then I have had problems like gel files
>jamming etc.

Sorry can't answer this one, I archive using a D2 DAT with no problems.

>4. Has anyone experienced problems with writing gel files over the
>network ?

I've had weird corrupted images on other macs, but I don't think it was 
to a network problem. I'm sure PE can answer this one though!!


Ian Ridgers

The DNA Sequencing Facility
Dept. of Zoology
The Natural History Museum
Cromwell Rd.
London. SW7 5BD

E-mail ir at nhm.ac.uk
Tel.44 -171 938 9297
Fax.44 -171 938 8754

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