TFBS search
by Tony Oosterveen
Hello,
I am just starting to use galaxy, and I was wondering if there is a
simple way to search genome wide for clustering of custom transcription
binding sites (preferentially with weight matrixes). All other programs
(~10) I have used till so far have their limitations, either the length
of the sequence they can handle is rather limited, they use only in
house transcription factor binding sites or they are not able to check
for evolutionary conservation.
Thanks,
Tony
Tony Oosterveen
Karolinska Institute
Stockholm
Sweden
13 years, 12 months
Looking For Tool DTD
by Scott Kuehn
Hello,
I'm looking for an appropriate DTD to use as a basis for designing new
tools (section 3, here: http://g2.trac.bx.psu.edu/wiki/AddToolTutorial).
Can someone point me toward this? I looked on the website and the latest
source distribution, and could not find anything.
Thanks,
Scott
Scott Kuehn
University of Washington Medical Genetics
2211 Elliot: 206-267-1091 x215
14 years
Sharing HIstories?
by Jacob Biesinger
Is it possible to share histories with other collaborators? I'd like them to
be able to see my data without having to step through the same steps as I
did to generate them. Can this be done in galaxy?
14 years
filter of 3'UTR conserved sequences
by Naum Gershenzon
Dear Sir/Madam,
I figured out how to retrieve all conserved human 3'UTR sequences from
Table Browser, however they came with multiple repetition (up to 5
times).
So my question is
“How can I filter these data in order to have all conserved human
3'UTR sequences WITHOUT DUPLICATION THE SAME SEQUEMCES MULTIPLE TIMES?”
Sincerely
Naum Gershenzon
14 years
feature requests
by Belinda M. Giardine
UCSC Genome Browser output with frame on left with links.
Able to upload as custom track at browser of choice
eg genome-test or dev browser, watson browser?, ...
implemented as url you can point your browser at?
Featured datasets
eg hard to load dbSNP, too large, keep local?
easy access to Ross and other local datasets
New Tools
To add chr for chroms (Ensembl doesn't include chr)
To get uniq rows from a dataset (cat sort uniq)
New join choice in Operate on Genomic Intervals
-treat interval fields separate so can keep interval file
on full join (will work with exact matches to intervals)
History
- A way of organizing the history into sections/folders,
can't just use new histories without reloading core queries,
when history is large it is hard to find which query you want when
many similar operations done,
- A way to archive a history, keep loaded datasets and how to run
operations (what was done) but not store all results indefinitely.
- When you open a history item could the display not return to the top.
14 years
