[Genome] Custom Tracks

[Kayla Smith]

Peter,

Please see the Custom Tracks FAQ here:

http://genome.ucsc.edu/goldenPath/help/customTrack.html

You will find Example 3 relevant.

I've converted the data you gave me into a format which shows shades of 
grey for your data.  I multiplied your p-values by 1000 so that you 
could see the gradient better.  Try pasting the custom track below into 
our custom track tool, or clicking here to see my session with this 
custom track:
http://genome.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kayla&hgS_otherUserSessionName=CT_for_Peter


browser position chr1:147973262-147975706
browser hide all
track name="Peter's BED track" description="Peter" visibility=2 
color=0,128,0 useScore=1

chr1	147973262	147973312	a 372.351348
chr1	147973300	147973350	b 372.351348
chr1	147973338	147973388	c 353.911558
chr1	147973376	147973426	d 335.036585
chr1	147973414	147973464	e 315.663303
chr1	147973452	147973502	f 295.71216
chr1	147973490	147973540	g 275.080532
chr1	147973528	147973578	h 253.632178
chr1	147974174	147974224	i 25.645723
chr1	147974212	147974262	j 1725.645723
chr1	147974858	147974908	k 83.74733
chr1	147975124	147975174	l 3822.09489
chr1	147975162	147975212	m 3409.069051
chr1	147975200	147975250	n 3064.172447
chr1	147975238	147975288	o 2771.80428
chr1	147975276	147975326	p 2520.802915
chr1	147975314	147975364	q 2302.969809
chr1	147975352	147975402	r 2112.146061
chr1	147975390	147975440	s 2112.146061
chr1	147975428	147975478	t 948.169009
chr1	147975466	147975516	u 178.606953
chr1	147975504	147975554	v 372.351348
chr1	147975542	147975592	w 372.351348
chr1	147975580	147975630	x 178.606953
chr1	147975618	147975668	y 178.606953
chr1	147975656	147975706	z 178.606953


I hope this helps you to visualize your data with our Custom Track 
tools.  Please don't hesitate to contact us again if you require further 
assistance.

Kayla Smith
UCSC Genome Bioinformatics Group



Peter Scacheri wrote:
> I'm trying to add a custom track with P-value scores.  How do I 
> display the track so that the scores are represented in different 
> shades of grey, ie., the higher the score, the darker the color. 
> Here is an example of my input file.
> 
> track name=test
> chr1	147973262	147973312	0.372351348
> chr1	147973300	147973350	0.372351348
> chr1	147973338	147973388	0.353911558
> chr1	147973376	147973426	0.335036585
> chr1	147973414	147973464	0.315663303
> chr1	147973452	147973502	0.29571216
> chr1	147973490	147973540	0.275080532
> chr1	147973528	147973578	0.253632178
> chr1	147974174	147974224	1.725645723
> chr1	147974212	147974262	1.725645723
> chr1	147974858	147974908	0.08374733
> chr1	147975124	147975174	3.82209489
> chr1	147975162	147975212	3.409069051
> chr1	147975200	147975250	3.064172447
> chr1	147975238	147975288	2.77180428
> chr1	147975276	147975326	2.520802915
> chr1	147975314	147975364	2.302969809
> chr1	147975352	147975402	2.112146061
> chr1	147975390	147975440	2.112146061
> chr1	147975428	147975478	0.948169009
> chr1	147975466	147975516	0.178606953
> chr1	147975504	147975554	0.372351348
> chr1	147975542	147975592	0.372351348
> chr1	147975580	147975630	0.178606953
> chr1	147975618	147975668	0.178606953
> chr1	147975656	147975706	0.178606953
> 
> 
> Thank you!
> Peter
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome