Hello,
There are several approaches to obtaining this type of data.
In the downloads area, there are a series of files you may find helpful,
such as:
http://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/
upstream1000.fa.gz - Sequences 1000 bases upstream of annotated
transcription starts for RefSeq genes with annotated 5' UTRs.
Also included in the annotation data set for mouse are several gene/gene
prediction data tracks. Reviewing the methods used to create each will
help you to determine which meet your needs. Do this by going to our
main browser page, clicking on Genomes in the top or side blue bar, and
choosing the mouse assembly. Submit at the default location and scroll
down to the track group "Genes and Gene Prediction Tracks". Click on a
track's name to view a description of contents, methods, and any display
controls. Tracks in other sections may also be helpful to you and are
definitely worth exploring.
To download this type of data, you can use the Table Browser ("Tables"
in top blue bar) to extract information in a customized format or go
into the Downloads area and ftp the appropriate table(s) that represent
the data. To understand the data contained in any table, use the TB
"view table schema" button.
Helpful links:
http://genome.ucsc.edu/
http://genome.ucsc.edu/cgi-bin/hgTables?command=start
http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
http://hgdownload.cse.ucsc.edu/downloads.html
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html
http://genome.ucsc.edu/FAQ/
We hope this helps to get you started. If you need any specific help
with a track or data type, please let us know,
Jennifer Jackson
UCSC Genome Bioinformatics Group
Gundala Viswanath wrote:
> Hi all,
>
> I have dowloaded a mouse genome (mm9)
> from Golden Path.
>
> Is there any additional table that list the location
> of TSS (transcription start site) in each chromosome?
>
> - Gundala Viswanath
> Jakarta - Indonesia
> _______________________________________________
> Genome maillist - [email protected]
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
Genome maillist - [email protected]
http://www.soe.ucsc.edu/mailman/listinfo/genome
