Question: How to add a custom color to BigWig files
1
gravatar for hss
4.1 years ago by
hss20
United States
hss20 wrote:

My wig files are too large for visualization in the UCSC browser.  I used the Galaxy utility Wig/BedGraph-to-bigWig  to convert my wig files.

I uploaded my wig file to the Galaxy workplace then ran the wig to bigWig conversion.   The resulting file can be displayed at UCSC main but the peaks are now just black.   When I select manage custom tracks in the UCSC browser

I see the configuration window but I cannot edit it to add the line color=0,200,0.  Is there a way to do this?   I tried downloading the bigwig file but it does not display as a simple text file so I am not sure how to proceed.  

Any suggestions will be greatly appreciated.

Cheers,

Scott  

galaxy • 3.4k views
ADD COMMENTlink modified 3.1 years ago by trinna220 • written 4.1 years ago by hss20
0
gravatar for Jennifer Hillman Jackson
4.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Color is designated on the track line of the wiggle file, before it is compressed into bigWig format. See the section "Parameters for custom wiggle track definition lines" on this UCSC FAQ: 
http://genome.ucsc.edu/goldenPath/help/wiggle.html

Some tips when using Galaxy:

  • compress one wiggle file at at time (one wiggle file per Galaxy dataset)
  • do not use browser lines. if you want to later specify a region or view, try using the Sessions function at UCSC
  • you can replace just the track line easily within Galaxy: Use "Text Manipulation" tools to remove the original track line, paste just a new single replacement line into the "Get Data -> Upload file" tool, then concatenate the two datasets together to create the updated wiggle file. Then compress to bigWig.

Best, Jen, Galaxy team

ADD COMMENTlink written 4.1 years ago by Jennifer Hillman Jackson25k

Hello,

I tried this concatenating strategy with a Bedgraph file (output of MACS2) before converting in BigWig with no success (pipeline below) https://biostar.usegalaxy.org/p/21389/

What would you recommand?

Thanks.

ADD REPLYlink written 18 months ago by leomachado9110

Did you edit/create a track line in the Bedgraph dataset to specify color? How-to is in the UCSC link above.

Did this fail conversion or was there some other problem?

If the conversion job failed, would you share the error message (click on the bug icon to view in full)? Was this at Galaxy Main (http://usegalaxy.org) or at some other Galaxy?

Thanks, Jen, Galaxy team

ADD REPLYlink written 18 months ago by Jennifer Hillman Jackson25k
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