multi-region visualization of structural variants

[Joana Fino]

Hi,

 

I have been testing the multi-region tool to display translocation regions, where in the same display I can have two regions of two different chromosomes.

I have been trying to apply the same concept, where one of the regions is inverted. For that,  I used the following configuration file:

 

https://cld.pt/dl/download/cf401f5f-556a-485a-a186-7db562300e69/inv%28der5%295q.txt

 

In this case I wanted that the chromosome 10 region started at 112483136 and ended at 100798030. When I use this configuration file it displays the two regions, without the inversion of the chromosome 10 region.

Is there any way to plot a inverted region?

 

 

Also, using the multi-region display, can I mark or highlight a deletion without removing the deleted zone in the configuration file?

 

Thank you for your time,

 

Joana Fino

 

[Brian Lee]

Dear Joana,

Thank you for using the UCSC Genome Browser and your question about inverting the view within your mulit-region selections.

Your input on how you are using our new multi-region tool is very helpful! At this time the regions can not be inverted, but we have created a ticket to investigate adding this feature. It is very useful to learn what investigators would like to see implemented and we greatly appreciate your input.

For highlighting a deletion or other region you might want to take advantage of adding custom tracks or the drag-and-select highlight option. Here is a session that has two custom tracks loaded, one with the configuration slices and another with some red annotations:http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.highlighting

Here are example custom tracks:

track name=Highlights  description="Adding custom tracks to mark regions" color=255,0,0
chr5 44597594 52030526  name1
chr5 34597594 40030526  name2
chr10 103828353 107392087 name3

track name=regions description="two regions as CustTracks" 
chr5 1 91561376 chr5 960 + 1 91561376 0 1 91561375, 0
chr10 100798030 112483136 chr10 960 - 100798030 112483136 0 1 11685106, 0

This session also has the drag-and-select highlight feature being used in the chromosome 10 region where you see a light blue bar. It also has the multi-region "Highlight alternating regions in multi-region view" option selected where each slice provided by the configuration file will be shaded alternating colors to help highlight slices.

I hope this information is useful to you and thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

--