I have just updated galaxy with the latest mercurial change sets and I
am having a few problems with the history.
The history is not automatically refreshing so new jobs appear to
still be queuing/running.
Also, I can't permanently delete an item from the history. It remains
with the message "This item has been deleted" even if I try to delete
it again. Is this a feature in the latest update.
Is anyone else having these problems?
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
No, this is a bug that had not quite made it out to our public
distribution, but it has now. Please update again, and you should
the fix. Sorry for the inconvenience.
Greg Von Kuster
Galaxy Development Team
I have in my project single end reads (50 bp) for some samples and
paired end reads (100 bp frw and rev) for the other samples. I had to
re-sequence some of the samples of which I have paired-end reads.
However the re-sequence data I receives is single-end reads of 250 bp.
Tophat wont allow mapping single and paired-end reads together. It
says the result will look bad. They do mention that you can convert
the junctions.bed file (output of Tophat) with bed_to_juncs using the
-j option. I quote for TopHat manual "run TopHat on the 2nd set of
reads using the -j option to supply the junctions file produced by
be_to_juncs in the previous step". This is supposed to work but I
didn't get it to work. Any suggestion on how I should go about
analyzing this data?
There are some performance problems with the Main site that we are
currently investigating. Thanks for the information and we apologize
for the problems.
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