Why does not Umap k100 (multi-read) contain X chromosome?

[yamawada]

Hello. I was looking at Umap k100 (multi-read) and noticed that it does not contain the X chromosome. Why is this?
Also, there is a notation error in line 15583132 that does not follow the bedgraph format.

[mehrankr]

Hello Ryuji-702,

Please specify which exact file you are referring to (URL).

Thanks,
Mehran

[yamawada]

Thank you for your quick reply.
Here's the link.
https://bismap.hoffmanlab.org/raw/hg19/k100.umap.bedgraph.gz

Thank you,
Ryuji-702

[mehrankr]

Thank you for reporting this.
I would have to look into this.

In the meantime, I checked the trackhub and it does contain a bigWig file with chromosome X as well.
There is likely a bug specific to the bedGraph you are referring to.

I recommend you to download the bigWig file from the trackhub:
List of all trackhub components for hg19:
https://bismap.hoffmanlab.org/trackhub/hg19/trackDb.txt

bigWig file corresponding to k100 umap:
https://www.pmgenomics.ca/hoffmanlab/proj/bismap/trackhub/hg19/k100.Umap.MultiTrackMappability.bw

It's better to convert that bigWig file to bedGraph and use it downstream.

Hope this helps.
Mehran