Jim Robinson

Hi Kate. First are you using g2nb, or just igv-jupyter stand alone? The URL error might be a CORS error (Cross Origin Resource Scripting) if the web host for the...

Hi @petermchale , I can't reproduce the issue with your original file. My test files are here: https://www.dropbox.com/scl/fi/27wueak6jfojdvf10794n/test.bedgraph?rlkey=uh3u9aemyxotsidu598jwszm6&dl=0, https://www.dropbox.com/scl/fi/4nqp7bhjk5zap7mqjwt4l/test.bw?rlkey=fx1b500fjiz0k1djmyipvf23f&dl=0. I created the bigwig as follows ``` bedGraphToBigWig test.bedgraph http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes test.bw...

Here's a comparisom between the bw and bedgraphs linked above with 2.19.4.

At that zoom IGV is probably not using zoom levels. If you convert the bigtools bigwig back to wig or bedgraph using UCSC's tools do you get the original file?

Ok, the difference then is probably something in zoom levels, as you suggest.

@jackh726 Its not doing this with the ucsc bigwig. You can see that if you zoom into base level.

It is deciding what zoom level to use, or whether to use a zoom level at all, based on the "reductionLevel" value for each zoom. This is compared with the...

I think the problem is with zoom level 0, which has a negative reduction level. I suspect you have an integer overflow bug.

Thanks for the heads up! On Fri, Nov 8, 2024 at 10:18 AM Colin Diesh ***@***.***> wrote: > fixed by this PR #144 > > — > Reply to this...