BED files - RGB support

Question

0

BED files - RGB support

asked 2013-09-25 15:13:30 -0600

This post is a wiki. Anyone with karma >75 is welcome to improve it.

Hello,

I'm trying to use different bed files downloaded from UCSC on GenomeBrowse and I would like to know if the software supports the itemRgb column at all. I've tried to input the color data either in RGB color values (200,0,0) or in integers (13107200), but none of them are recognized by GenomeBrowse.

Is this feature going to be implemented in GenomeBrowse in future?

Thanks a lot

Oswaldo Lorenzo

edit retag flag offensive close merge delete

Accepted Answer

0

answered 2013-09-30 08:44:55 -0600

Gabe Rudy
90 ●1 ●4 ●6 http://blog.goldenhelix.c...

Hey Oswaldo,

We do support itemRgb. We expect the RGB colors to be encoded like numbers 200,0,0 (no parens).

We also expect the itemRgb="on" key/val pair on the 'track' line of the file. For example, here is a couple lines of a file that we render with color:

track itemRgb="On"
chr7    54028   73584   uc003sii.2  0   -   54028   54028   255,0,0 .   AL137655
chr7    60328   61569   uc010krx.1  0   -   60328   60328   255,0,0 .   PDGFA
chr7    62967   63529   uc003sij.2  0   -   62967   63366   255,0,0 .   DQ576410
chr7    64068   64107   uc003sil.1  0   -   64068   64068   255,0,0 .   DQ584609
chr7    65159   65220   uc003sim.1  0   -   65159   65159   255,0,0 .   DQ600587
chr7    75460   116489  uc003sin.1  0   -   75460   75460   255,0,0 .   AL137655
chr7    244679  249951  uc003sio.1  0   +   244679  244679  0,255,0 .   AK024243
chr7    244826  249951  uc010kry.1  0   +   244826  244826  0,255,0 .   AK310146

I hope that helps.

-Gabe

edit flag offensive delete link

Answer 2

0

answered 2013-09-30 12:33:58 -0600

This post is a wiki. Anyone with karma >75 is welcome to improve it.

Hello Gabe,

I didn't know I had to specify the option itemRgb="on" key/val pair on the 'track' line of the file. Of course it helped. Now it works.

Thank you very much,

Best

Oswaldo

edit flag offensive delete link

BED files - RGB support

2 answers

Question Tools

Stats

Related questions