method for 5mC data

[Eric-Y-S]

I have some questions about the epigenetic data for v2 primates assembly.

For example, at https://genomeark.s3.amazonaws.com/index.html?prefix=species/Pan_paniscus/mPanPan1/assembly_curated/epi/ there are 3 files:

• Is there any significant difference between the results from minimap and winnowmap? Does the tag "CpG" in the name of minimap result indicate the removal of 5mC that are outside of CpG region?

• How can I access the processing method used for these calling result? In the paper [Makova, K.D., Pickett, B.D., Harris, R.S. et al. The complete sequence and comparative analysis of ape sex chromosomes. Nature 630, 401–411 (2024). https://doi.org/10.1038/s41586-024-07473-2], winnowmap is mentioned, but without mention of minimap.

• How are the scores calculated? Well, it seems to be a percentage... But is there any detail for the computational formula?

Thanks!

[arangrhie]

Hi @Eric-Y-S , you can find better descriptions here.
The track descriptions and link to the T2T browser can be found here.
We haven't done a thorough comparison between the most recent minimap2 and winnowmap2, but by that time, winnowmap2 was yielding better alignments in repetetive region.

Arang

[Eric-Y-S]

OK @arangrhie, Thanks🙂