Empty track from gtf file

[Evan Henneberry]

Hello,

I am trying to visualize variants within sorted gtf files generated from cufflinks. When I load them into IGV, nothing is displayed. I have tried zooming in on many regions, set feature visibility window to 0 to see all the genes, and still nothing.

I can see the Ref Seq genes, so that is ok, but for my data there is nothing showing up.

Any idea why this is occurring?

Thanks

[James Robinson]

Do the sequence (chromosome) names in your gtf file match those in the reference you are viewing?   If they do you'll need to post the file,  don't copy & paste it into a post as whitespace is lost.

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[James Robinson]

This file loads correctly (see screenshot).   It contains a lot of transcript records in the same location of chr11.    I'm not sure what you are expecting to see.

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On Fri, Jul 28, 2017 at 2:16 AM, Evan Henneberry <evan.he...@gmail.com> wrote:

Hello,

Yes, the chromosome names match the reference. I attached the file.

Thanks

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[Evan Henneberry]

Hi Jim,

That is exactly what I expect to see. For some reason, it was not showing up in the track. However, I indeed now do see it as well.

Thanks for the help!

Dana petak, 28. srpnja 2017. u 16:07:12 UTC+2, korisnik Jim Robinson napisao je:

This file loads correctly (see screenshot).   It contains a lot of transcript records in the same location of chr11.    I'm not sure what you are expecting to see.

​

On Fri, Jul 28, 2017 at 2:16 AM, Evan Henneberry <evan.he...@gmail.com> wrote:

Hello,

Yes, the chromosome names match the reference. I attached the file.

Thanks

Dana srijeda, 26. srpnja 2017. u 10:14:18 UTC+2, korisnik Evan Henneberry napisao je:

Hello,

I am trying to visualize variants within sorted gtf files generated from cufflinks. When I load them into IGV, nothing is displayed. I have tried zooming in on many regions, set feature visibility window to 0 to see all the genes, and still nothing.

I can see the Ref Seq genes, so that is ok, but for my data there is nothing showing up.

Any idea why this is occurring?

Thanks

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