BigWigs tracks have incorrect chromosome order

[mchikina]

I cannot seem to get BigWigs to be loaded in the correct chromosomal order. The BigWig file if from ENCODE. Initially I used official UCSC chrom.sizes -- that did not work. I made a new chrom.sizes file that corresponds exactly to what I get by running bigWigInfo on my BigWig that also didn't work. It is easy to see that the chromosomes are out of order when you zoom out to whole genome view. The data gaps should line up across BigWig and HiC -- the do not.

What are the instructions for making all of this line up.

[pkerpedjiev]

Sorry for the delayed response, could you try adding a chromsizes file?

Instructions are here:

https://docs.higlass.io/data_preparation.html#bigwig-files

[mchikina]

Thanks for the quick reply. Yes, I did exactly that and tried two different versions (see my message above). In both cases the result was out of order.

[pkerpedjiev]

OK, so this project hasn't been maintained in a while so I'll plug resgen.io, the successor I've been maintaining. It uses the higlass browsers and adds some data management on top. If you'd like to try it there's a local version that you can run on your own machine so your data stays where it is. To view a bigwig you would do the following:

1. Copy your bigwig to its own directory (cd my.bigwig ~/my_directory)
2. Copy your chromsizes to the same directory (cd my.chrom.sizes ~/my_directory)
3. Install resgen-python (pip install resgen-python)
4. Go to your local directory and start resgen (cd ~/my_directory && resgen manage start .)
5. Create a local resgen user (resgen manage create-user)
6. Sync your local datasets to the running resgen instance (resgen manage sync-datasets .)
7. Open your local resgen (resgen manage open .)
8. Drag your datasets into the viewer

The docs for this can be found at https://docs.resgen.io/local/running-locally/.

See video below for an example.

Screen.Recording.2025-12-18.at.10.09.45.PM.mov

Finally, full disclaimer, this tool requires a license for use in a directory with more than 10 files. Since the local version is still being developed I'm happy to give you a free license if it's useful for you.

[mchikina]

Thanks a lot! I will definitely try it out. I would very much appreciate the free license.

[pkerpedjiev]

For sure! Shoot me an email at pete@resgen.io and I'll send you a license file and help with any issues you may have.