ChrY absent from IGV but present in BigWig file

[Carl de Boer]

I'm having a curious problem. I have many samples and created bigwig files for each, but in displaying these tracks on IGV, some samples appear to be missing data for chrY (hg38) even though the data are present in the bigwig file. 

Below is shown two bigwig files (the second just manually re-running the same bedGraphToBigWig command as our pipeline used) and a tdf file, all for the same data. The tdf file was made from the bigwig file (bigWigToWiggle -> igvtools toTDF).  

In addition to making the TDF file from the BW file, I also manually confirmed that the chrY reads are present in the bedgraph before converting to bigwig and after, by converting the bigwig back to a wiggle or bedgraph. The data are present, it's just not being displayed by IGV.   I could also find no differences between the bigwigs of samples where chrY is displayed and those where it was not, and could find no other chromosomes where data was missing.  The bigwigs were all made by the same pipeline and the data look similar, but in some chrY is missing.

IGV is version 2.3.81.

Thanks!

[James Robinson]

That is curious.  Would it be possible to share the bigwig file?  I can send a dropbox link if its not too huge.   Do you only find this problem on chrY?

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[Carl de Boer]

Yeah, that should be fine.  I will email you with a link to it on the Broad cluster.

On Friday, November 4, 2016 at 7:07:40 PM UTC-4, Jim Robinson wrote:

That is curious.  Would it be possible to share the bigwig file?  I can send a dropbox link if its not too huge.   Do you only find this problem on chrY?

On Fri, Nov 4, 2016 at 12:49 PM, Carl de Boer <cgde...@broadinstitute.org> wrote:

I'm having a curious problem. I have many samples and created bigwig files for each, but in displaying these tracks on IGV, some samples appear to be missing data for chrY (hg38) even though the data are present in the bigwig file. 

Below is shown two bigwig files (the second just manually re-running the same bedGraphToBigWig command as our pipeline used) and a tdf file, all for the same data. The tdf file was made from the bigwig file (bigWigToWiggle -> igvtools toTDF).  

In addition to making the TDF file from the BW file, I also manually confirmed that the chrY reads are present in the bedgraph before converting to bigwig and after, by converting the bigwig back to a wiggle or bedgraph. The data are present, it's just not being displayed by IGV.   I could also find no differences between the bigwigs of samples where chrY is displayed and those where it was not, and could find no other chromosomes where data was missing.  The bigwigs were all made by the same pipeline and the data look similar, but in some chrY is missing.

IGV is version 2.3.81.

Thanks!

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[James Robinson]

Carl, this should be fixed, the release number is 2.3.87.  Give it a try and let me know if you have further issues.

[Carl de Boer]

It looks good with that version.  Thanks, Jim!