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Question: Trackster and TopHat
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gravatar for Suzanne Gomes
4.3 years ago by
Suzanne Gomes • 120
Canada
Suzanne Gomes • 120 wrote:

Hi,

I'm looking at some data in Trackster and I'm a bit confused about the sense/antisense labels on my data from TopHat. It looks like a single RNA-seq read is (almost always) partially assigned to sense and partially to the antisense strand. But I assume that TopHat doesn't report a read unless it is mapped to just one strand, because that would make no sense. Any idea what I'm seeing here?

I'd attach a picture to show what I'm talking about but I can't figure out how... so any help on how to do that would also be appreciated. Why is there only an option to upload a URL?

Thanks

Suzanne
rna-seq trackster • 752 views
ADD COMMENT • link •
modified 4.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.3 years ago by Suzanne Gomes • 120
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gravatar for Jennifer Hillman Jackson
4.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The URL is so you put your picture on a server that can serve a file. We can't upload graphics. 

I am guessing that you are talking about paired reads? One is most likely aligning in the forward orientation and the other in the reverse, like this (same strand). 

(+) --------->     <---------  (-)

If this is not what you are describing, and the matches are primary and spliced (Tophat can be configured to report sub-hits - these can align anywhere if the setting are permissive enough and will not be used by downstream tools in the RNA-seq group, so can be ignored, or better not even captured to start with), then you can send a link to a shared Visualization on the public Main instance (http://usegalaxy.org) to our email galaxy-bugs@bx.psu.edu. Please note the coordinates where you are seeing the issue and include a link to this post, so we can match the two.

Best, Jen, Galaxy team
ADD COMMENT • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k
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