change color
Hidemi Kajimoto
Hello,
I have some questions to prepare figures for manuscript. Data is ChIP-seq.
1. I would like to change peak’s color.
2. I would like to delete fine vertical lines.
3. I would like to delete information of the genes except Myh6.
I attached picture below.
Thanks,
Hidemi
Jairo Navarro Gonzalez
Hello Hidemi,
Thank you for using the UCSC Genome Browser and your questions to prepare figures for your manuscript.
Changing a custom track's color:
You can change the color of your annotation track by using the color=<RRR,GGG,BBB> attribute=value pair for your custom track. This setting defines the main color for the annotation track and the color consists of three comma-separated RGB values from 0-255. The default value is 0,0,0 (black).
For example, to make your peaks red, your new track line for your custom track will be:
Removing fine vertical lines
To remove the fine vertical lines from the background, you can customize the PDF output by changing the configuration settings from this page:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgTracksConfigPage=configure
Once on that page, uncheck: Show light blue vertical guidelines, or light red vertical window separators in multi-region view
Display only relevant information from genes (Myh6).
To display only the relevant gene information, you will have to create a custom track of these gene annotations using the Table Browser. First, navigate to the Table Browser and select your assembly. I used the following settings:
clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions
track: UCSC Genes
table: knownGene
region: genome
output format: custom track
Next, to only display your gene of interest, click the paste list button that is beside the identifiers (names/accessions) setting, and then paste in your gene name, Myh6. After you have entered your gene list, click the submit button. Once back on the main Table Browser page, click get output. This will take you to a new page where you can create a BED record for each whole gene. Finally, you can view the track in the Browser or download the file to make other modifications to the track line, such as changing the default black color for custom tracks.
If you would like to know more about the different custom track settings you can use, please refer to our Genome Browser User's Guide.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genomics Institute
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