Parts of tracks are not shown in IGV

[Katja Hebestreit]

Hello,

It seems that sometimes parts of tracks are not shown in the IGV although I can see the respective rows in the BED file. But when I create a small subset of this BED file the IGV DO show these parts. Thus, I assume that this problem might exist for big BED files only.
I am using IGV 2.1.21.

Since the BED file of question is 200MB of size I can not attach it here. Please contact me and I will provide it.

Thank you!
Best,
Katja

[Jacob Silterra]

Hi Katja,

[Note: User has provided data file privately].

It looks like this is a problem with indexing. When the file is indexed several features in the neighborhood of chr1:145139645 do not appear, when it is not indexed they do. I've filed this in our issue tracker at https://github.com/broadinstitute/IGV/issues/14.

As a temporary fix, you can delete the bed index file and those features will show up. This can cause some serious usability problems as it will require a lot more memory by IGV.

-Jacob

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Jacob Silterra
Software Engineer
Broad Institute

[Jacob Silterra]

The problem was actually that the input BED file was not sorted. Attempting to create an index of an unsorted file should have thrown an error, but didn't. See GitHub issue #14 for details (resolved as of this writing).

On Thursday, August 23, 2012 11:41:15 AM UTC-4, Jacob Silterra wrote:

Hi Katja,

[Note: User has provided data file privately].

It looks like this is a problem with indexing. When the file is indexed several features in the neighborhood of chr1:145139645 do not appear, when it is not indexed they do. I've filed this in our issue tracker at https://github.com/broadinstitute/IGV/issues/14.

As a temporary fix, you can delete the bed index file and those features will show up. This can cause some serious usability problems as it will require a lot more memory by IGV.

-Jacob