[Galaxy-user] extracting opossum sequences from UCSC Test browser

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

[Galaxy-user] extracting opossum sequences from UCSC Test browser

Melissa Wilson
The opossum sequence is assembled into chromosomes in the UCSC test browser, but
I am, thus far, unable to extract the nucleotide sequence that corresponds to a
given  chromosomal location.  

Previously when I went to "Get Data"  at the most recent opossum assembly in the
test browser it would act as if it were extracting the BED file, but there
would be " # no results from query" and I could not extract the genomic
sequence corresponding to my chromosomal location (chr7:32478949-32483556) in
opossum.  The query turned red and I received the following error message:  "An
error occurred running this job: <font color="yellow">BED fields are missing.
Possibly no strand information is present</font>.  I assume this is because no
BED file was actually extracted from the table browser.

Now, when I "Get Data"  from the UCSC Test browser now I can't even get to the
most recent opossum data in the UCSC test browser.  When I try to switch from
Human to Opossum I am sent to the "UCSC Table Browser" page with the statement,
"This is a proxy to the data services provided by the UCSC Genome Browser's
Table Browser"  

Is there a different way to extract the sequences corresponding to the current
assembly of the opossum genome?

Thank-you very much,