Support BED input?

[PanZiwei]

Hi,
Thanks for the amazing tool. I already have per-site methylation calling results from long-read sequencing in BED format with chromosome, start position, end position, and methylation frequency for each CpG site.

Is it possible to use the BED file as metheor input for methylation heterogeneity measures analysis? Any hints for the implementation? Thanks.

[little-spice]

The BED file lacks information about reads, thus I believe it cannot be utilized as input for calculating heterogeneity.

[dohlee]

Yes, metheor is designed to deal with CpG methylation patterns extracted from sequencing reads, so BED file would not be the best format for that.