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Question: Trackster not showing alignments
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gravatar for mike.thon
3.8 years ago by
mike.thon • 30
University of Salamanca, Spain
mike.thon • 30 wrote:

I'm trying to visualize a BAM file made with tophat2 using trackster. When I click on the Visualize with Trackster button, trackster opens and I can see only a histogram. If I zoom in a few levels the histogram disappears.  How can I view individual reads with Trackster?

 

Note that I used tophat2 to align reads to a genome sequence in my history. Then I used that sequence to creat a custom build in my account.  Then I associated the custom build with the BAM file from tophat2 before visualizing with trackster.
trackster bam • 966 views
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modified 3.8 years ago • written 3.8 years ago by mike.thon • 30
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gravatar for Hotz, Hans-Rudolf
3.8 years ago by
Hotz, Hans-Rudolf • 1.8k
Switzerland
Hotz, Hans-Rudolf • 1.8k wrote:

change the "set Display Mode" (the first icon to the right of the track label - you might need to mouse over the label first in order to see the icons) to 'Pack' or 'Squish'.

 

Regards, Hans-Rudolf

 
ADD COMMENT • link written 3.8 years ago by Hotz, Hans-Rudolf • 1.8k

I tried that but it doesn't change the display.  I should point out that this is a local installation of Galaxy and I'm the admin. I don't know if there are other tools that need to be installed to get Trackster to work. 

ADD REPLY • link written 3.8 years ago by mike.thon • 30

well, we sometimes also get just a blank track on our local Galaxy server, which we can't explain :(  reducing the file size (e.g. sampling the bam file) sometimes helps.

Have you tried trackster with a BAM file from a built in genome?

Hans-Rudolf

 

 

 

ADD REPLY • link written 3.8 years ago by Hotz, Hans-Rudolf • 1.8k
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