[Genome] order/ custom tracks

[Pauline Fujita]

Hello Minou,

If you have more than one item under a single heading in your bed file, 
for example:

track name="tb_gold" description="table browser query on gold" 
visibility=3 url=
chrX    151051262    151153933    AC116666.2    0    +
chrX    151153933    151304010    AF282854.4    0    +
chrX    151304010    151485145    AC108171.3    0    +

the browser will automatically order the items vertically according to 
their left to right  position on the genome. If you want to control the 
vertical order in which items appear, independent of their genome 
position, you will need to split the items up into separate tracks. You 
can do this by putting a separate header before each entry in your bed file:

track name="tb_gold1" description="table browser query on gold" 
visibility=3 url=
chrX    151051262    151153933    AC116666.2    0    +
track name="tb_gold2" description="table browser query on gold" 
visibility=3 url=
chrX    151153933    151304010    AF282854.4    0    +
track name="tb_gold3" description="table browser query on gold" 
visibility=3 url=
chrX    151304010    151485145    AC108171.3    0    +

Note that each header should have a different track name (track 
name="tb_gold1,2,3").

Once you have the items as separate tracks you can change the order in 
which any tracks (including custom tracks) appear in the browser by 
clicking on the "configure" button located just below the browser 
display. In the configure menu, make sure the "Enable track re-ordering" 
option (in the "configure image" section) is checked. Once checked, you 
should see a "group order" column beside each of the tracks and by 
changing the number that appears beside the track in the order column 
you change the order in which it will be displayed. A smaller number 
gives a track a higher priority thus displaying it closer to the top.

Hopefully this information was helpful and answers your question. If you 
have further questions or require clarification feel free to contact the 
mailing list at genome at soe.ucsc.edu.

Regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

bina at purdue.edu wrote:
> Hello
>
> I have loaded a .bed file for displaying 3 custom tracks on the HG browser
>
> The Browser is changing the order in which the three tracks are displayed 
>
> How can I fix this problem?
>
> Minou Bina
> Purdue University  
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