LINE

[Nayeck, Jaykar (NIH/NICHD) [F]]

Hi,

 

I’m trying to only view the LINE from the RepeatMaser for the whole X chromosome, is there any possible way without having to zoom in and see everything?

 

Thanks,

Jaykar N.

[Steve Heitner]

Hello, Jaykar.

There is no way to do this with the standard Browser track, but you can create a custom track using the Table Browser to isolate the LINE elements and then view your custom track in the Browser.  If you’re unfamiliar with the Table Browser, please see the User’s Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.

To create your custom track, perform the following steps:

1. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables

2. Select the following options:
Clade: Mammal
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Variation and Repeats
Track: RepeatMasker
Table: rmsk
Region: select “position” and enter chrX in the text box
Output format: custom track

3. On the “filter” line, click the “create” button

4. Change the “repClass” line so that it reads the following: repClass does match LINE

5. Click the “submit” button

6. You can change the custom track description or just accept the default settings

7. Click the “get custom track in genome browser” button

8. Your track will appear in the Browser as “table browser query on rmsk” (or whatever you renamed it to if you renamed it in step 6).  There will also be a new track group below the Browser’s graphical display titled “Custom Tracks” which will contain your custom track.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.

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Steve Heitner
UCSC Genome Bioinformatics Group

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