Question: UCSC itemRgb on column 9
0
gravatar for varsha619
6 months ago by
varsha61970
varsha61970 wrote:

Hello, I am trying to set colors to my bed track based on column values using itemRgb on option. I have 1st 3 columns in my bed file for chrom, chromStart and chromEnd, 4th column has the values and 5th column has color codes for rgb for example 0,0,255. I converted the bed to bb format and used -

track XYZ

type bigBed

visibility full

itemRgb on

I am able to view the track all in black but not with the colors I want. Is it because my Rgb color values are not in column 9? Do I have to use all 9 columns mentioned here https://useast.ensembl.org/info/website/upload/bed.html to be able to use itemRgb or can I specify that the 5th column has the Rgb values? If I need all 9 columns, can the other column values be . or NA? Please let me know, I appreciate your help!

itemrgb ucsc • 258 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by varsha61970

it's clearly defined in https://genome.ucsc.edu/FAQ/FAQformat.html#format1

ADD REPLYlink written 6 months ago by Pierre Lindenbaum119k

You need to have the thickStart and thickEnd to start the drawing

chr7  127471196  127472363  Pos1  0  +  127471196  127472363  255,0,0

Chrom, Start, End, Name, Score, Strand, ThickStart, ThickEnd, itemRgb

You already have Chrom, Start, End, Score and itemRgb

Name could be : A, B, C, D whatever you want

Strand : if you don't care set + for all

ThickStart/ThickEnd are the same as Start/End if you want to visualize the whole item

ADD REPLYlink modified 6 months ago • written 6 months ago by Bastien Hervé4.0k

I used Chrom, Start, End columns, column 4 and 5 are the same (scores), column 6 is ".", columns 7 and 8 are the same as columns 2 and 3, and column 9 is Rgb code. I still don't see the colors in my track, my visibility is full and itemRgb on. I am not sure what I am missing here. Thank you for your help!

ADD REPLYlink written 6 months ago by varsha61970

Can you detail your steps to upload your file and display it to UCSC ?

I don't have a web server to try this on my own... Did you follow all the steps in this doc

Could you upload a screenshot of your UCSC and the inside of your bed file please

ADD REPLYlink written 6 months ago by Bastien Hervé4.0k

Yes I did follow the steps in the link and my bed file example is as follows (Drosophila genome) -

chr2L   7597    7617    4.62708799702989    4.62708799702989    .   7597    7617    255,0,0

chr2L   10912   10932   5   5   .   10912   10932   0,0,255

chr2L   17527   17547   4.76955107862173    4.76955107862173    .   17527   17547   255,0,0
ADD REPLYlink modified 6 months ago • written 6 months ago by varsha61970

What your UCSC visualization looks like ?

ADD REPLYlink written 6 months ago by Bastien Hervé4.0k

They look fine except for all tracks in black and not color, sorry I am unable to upload a screenshot here.

ADD REPLYlink written 6 months ago by varsha61970

How to add images to a Biostars post

ADD REPLYlink written 6 months ago by Bastien Hervé4.0k
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