[Genome] Sense/antisense genes

[nham tran]

Dear Ann,

I am a novice trying to find antisense and sense pairs. I search the 
archives and found your advice on the archives. Can i ask you some 
specific questions about the task.

Step One.  Make a Custom Track with all of the genes on the positive strand.

1. Navigate to the Table Browser ("Tables" in the blue navigation bar
across the top of the browser).

2. Configure like so:
clade: vertebrate
genome: human
assembly: Mar. 2006 (assuming you want the latest human assembly)
group: Genes and Gene Prediction Tracks
track: UCSC Genes (or choose another gene track here)
table: knownGene
region: genome

3. filter:  strand does match +

4. output format: custom track

5. name the custom track (ie sense)

*6. HIT the output button*

6. get the custom track in table browser.  *This will take you back to 
the table browser.* Now your custom track of all
positive-strand genes is available in both the Table Browser and for 
viewing in the Genome Browser. *I cannot see the custom track in the 
table browers*


Step Two.  Repeat step one for genes on the negative strand,* but for 
step 3. filter:  strand does match - (is this correct)*


Step Three.  Intersect the positive and negative Custom Tracks.
1. Use the Table Browser again.

2. Choose the positive-strand custom track from the table browser controls.
*Here is the problem, I cannot find the name tracks "sense" or antisense 
in the table browers. Can you help. *

3. Press the intersect button and choose the negative-strand custom
track from this page.  Leave the first choice checked "All AAA records
that have any overlap with BBB".  Press submit.

Many thanks

Nham

-- 
Nham Tran PhD

Address:
Vascular Biology (Room 5.39)
Centenary Institute of Cancer Medicine and Cell Biology
University of Sydney
NSW 2042

Phone 61 2 9565 6226