Some hg38 Bismap k100 tracks do not contain chr1 or chr2

[njspix]

For instance, the bismap hg38 single-read k100 file from https://bismap.hoffmanlab.org/ :

[mehrankr]

Hello,

Please use the tracks available at UCSC genome browser mappability track.
Also, could you mention where you downloaded these incomplete tracks from?

Best,
Mehran

[njspix]

Hello Mehran,

The incomplete track was downloaded from https://bismap.hoffmanlab.org/raw/hg38/k100.bismap.bed.gz. I tried to use the UCSC tracks, but was unable to find a way to access them programmatically. Ideally I would love to have a (semi)-permanent online resource to point my scripts to, which will always give the same version of the track.

[mehrankr]

Sorry about this problem. I looked into the folder and both bedgraph.gz and wg.gz files don't have this issue.
Please use those files for now since they are complete and don't have that issue.

Those files are more complete than the BED version;
The BED version basically thresholds those files with >0 to include/exclude genomic regions.

In addition, the .uint files https://bismap.hoffmanlab.org/raw/uint/hg38/ are the best for programmatic access
You can see the code for using them here:

https://github.com/hoffmangroup/umap/blob/master/umap/uint8_to_bed_parallel.py#L280

[njspix]

Thank you for the information! I am using the multi-read bed files for now.