how to create personel track sets regardless of genomic positions.

[Anita Tranberg Simonsen]

Dear UCSC

 

I am analyzing microarray data using the Agilent CytoGenomics software and through that we can access the UCSC browser when a CNV in question is to be evaluated in a patient sample. The specific CNV then open and is marked as a User track in UCSC, however sometimes the setup has returned to default and is then different from last time I used the UCSC site. Is there an explanation for that?

 

I want to create a session with specific tracks for analysis, however when constructing a My session it is defined of the chromosomal position which it is generated from. So when I go to the UCSC site through Cytogenomics I have the My track at the top, however when I load My session with the tracks I want to use for analysis, the software jumps to another place in the genome and I shall then type in the genomic coordinates manually.  

 

My question is therefore:

Is it possible to create a session (or something else) including the specific databases/tracks to apply to a custom track opened through the Cytogenomics software without being connected to a specific genomic position?

 

I know it is possible when using the recommended track sets, but I cannot figure out how to create my own track set independent on a genomic position.

 

Finally, is it possible to change a username but keep the user on the same email?

 

Looking forward to hear from you,

¨

Kind regards,

Anita

 

Anita Tranberg Simonsen

Molekylærbiolog, PhD

Tel. +45 7845 5565

anit...@rm.dk

Klinisk Genetisk Afdeling ▪ Region Midtjylland

Brendstrupgårdsvej 21C, Skejby ▪ DK-8200 Aarhus N

 

 

[Robert Kuhn]

Dear Anita,

I will let the Browser staff reply to your question directly, but I thought I would

point out to you a set of videos about links that I made several years go when I 

was still working at the Genome Browser.  They address specifically some ways 

to configure links.  Each video has a transcript so you can see the topics without

having to watch the whole vid, with a way to jump to the desired point in the video.  

The first video in the series is here:

https://www.youtube.com/watch?v=p6TPvHDmpJk&list=UUQnUJepyNOw0p8s2otX4RYQ&index=1&t=0s

best wishes,

   --b0b kuhn

Robert Kuhn, PhD

Associate Director UCSC Genome Browser (retired)

dba Robert Kuhn Consulting

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[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

Custom tracks are removed 48 hours after the last time they were accessed unless they are saved in a session. Your settings for the UCSC Genome Browser, such as which tracks are on/off, are controlled through a variable called "hgsid". You can find this variable in the URL, and it looks like:

&hgsid=2437351821_Y09XgAA1cikdvRLhxrYevVJUiM5D

If you share a URL with this variable with others, then any changes they make will also be reflected in your instance. Removing this variable and reloading the page will assign a new hgsid and is another way to create independent tabs on your web browser. More information about the hgsid can be found on the following help page:

https://genome.ucsc.edu/FAQ/FAQlink.html#hgsid

When you click on one of the Recommended Track Sets, there are URL variables that control the position and display of the data. For example, if you were to use the following session URL:

http://genome.ucsc.edu/s/view/clinicalzoom

You can add URL parameters such as position=chr7:75,627,863-75,677,298 to control the coordinates for the session:

http://genome.ucsc.edu/s/view/clinicalzoom?position=chr7:75,627,863-75,677,298

A full list of URL parameters can be found on the following help page:

https://genome.ucsc.edu/FAQ/FAQlink.html

We would also be more than happy to update the username on our end. We simply need to know what to change and for which email.

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 Genome Browser

To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAG3hb9uEncGo5yZfTU5_%2BLG0Dmq_%2BgvDEZn_FvLyzCsqTwwj%2Bg%40mail.gmail.com.