Hi Hannah,
Just wanted to let you know that we added a CpG Islands track for
platypus/ornAna1 today.
-
Greg Roe
UCSC Genome Bioinformatics Group
On 11/22/11 4:17 PM, Vanessa Kirkup Swing wrote:
> Hi Hannah,
>
> We currently don't have the CpG island track for platypus. We have put your
> requ
Hi Diego,
Most of our bigBed/bigWig/bam files used by our database entries are
available via URLs somewhere in the hierarchy:
http://hgdownload.cse.ucsc.edu/gbdb/
The files that you see in the database schema, for example:
/gbdb/some/path/name.bigFile
can be found on our downloads site:
http://
Hi again,
It turns out that we are able to support older VCF formats (3.* and
above), but there was a bug in the parser for the older format. We
fixed the bug, and the fix will be out on our website within a few
weeks. In the meantime, you can use our test server,
http://genome-test.cse.ucsc
Few more questions about this topic...
The aforementioned files (bigBed, BigWig and bam) are intended to be used
just internally by the UCSC people or external users like me can do
something with them?
If the last is true, where can I find information about the usability?
Thanks,
Diego
-Origin
Hello, Gordon.
One of our engineers mentioned that whether or not a table has a
range/values link is, among other things, a function of table size. The
RepeatMasker table for hg19 is about 13 times larger than the same table in
hg18 which explains the absence of the range/value links in hg19.
Pr
Hi Peter,
One of our engineers mentioned the BED 4-6 option was added to the
multiple option because this was requested by ENCODE users. However for
BED12, he says "[looking at the code] if the range find on the chain
returns two or more top-scoring chains of the same score, it calls it
"dupli
Hello,
In the Table Browser, while viewing a "table schema", there used to be links to
show all possible values.
It seems that in some tables in the current version of genome browser, these
links are missing - or perhaps I'm doing something wrong ?
Compare:
hg19 Human mRNA table - it has the "
Hi Juliana,
Selecting "sequence" in the Table Browser only ever outputs genomic
(reference) sequence (apart from a few instances where select RNA and/or
protein sequence is an option). This is the reason you only see "A".
On of our engineers looked at this one and commented:
"The user is proba
Good Morning Rad:
Please note the discussion about the shell environment variables MYSQLINC and
MYSQLLIBS
in the instructions step 3 in the source file:
src/product/README.building.source
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/product/README.building.source
--Hiram
M
Hi Clayton,
Galaxy (http://main.g2.bx.psu.edu/) has some tools that you are interested
in. They have some GTF/GFF tools under the "Filter and Sort" menu. If you
have questions about these tools you will need to contact them:
galaxy-u...@lists.bx.psu.edu.
If you are interested in using data from o
Dear Brooke, dear all,
thanks a lot for your fast help,
cheers,
Carsten
> Hi Carsten,
>
> These questions about SAM format should really be directed to the
> samtools-help list rather than the Genome Browser help list.
>
> However, one of our engineers explained what you are seeing:
>
> "This i
Hello everyone,
I am interested in using hgWiggle program, so I downloaded jkent package and
trying to build the pogram from the source
I have a compilation error which says :
../../../lib/x86_64/jkhgap.a(jksql.o): In function `sqlEscapeString2':
/fs/sh-code/Software/JKENT/src/hg/lib/jksql.c:20
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