Look into whether a higlass track data file already exists for visualization of genome mappability scores

[keller-mark]

Users may want to visualize the genome mappability confidence values as a separate track.

The data for such a track may already be available through the public higlass server. But if it is not, we should look into creating it and uploading it to the higlass server.

[keller-mark]

See https://sites.google.com/site/anshulkundaje/projects/blacklists

[keller-mark]

It looks like there may be mouse mm9 files in higlass already, but no other genome assemblies.

[keller-mark]

It looks like the Ballinger2019 100mer Mapability track already in higlass is good for the hg19 case. I also created two snakemake workflows for processing the mappability BED files from these two sources:

• Karimzadeh2018 https://bismap.hoffmanlab.org/
• Boyle2018 https://github.com/Boyle-Lab/Blacklist/tree/master/lists

The code I wrote is here: https://github.com/keller-mark/cistrome-clodius-mappability

[keller-mark]

This shows 3 tracks:

• the existing Ballinger2019 track in the public higlass server instance
• Karimzadeh2018-hg19-k100.umap.bed.multires
• Boyle2018-hg19-blacklist.v2.bed.multires