Hi all.

I have some histone marks (H3K27ac and H3K27me3) as well as DNA methylation (whole genome bisulfite sequencing) data for the entire genome in some samples. I am aware of the variability and repeats issue in the HLA region that causes complications in read mapping. There are tools out there like HISAT2 for mapping DNASeq or RNASeq data that uses graph genome and takes the HLA region issues into consideration. All the publications out there, have been using HISAT2 or other "HAL region aware" tools for DNASeq and RNASeq, HOWEVER, when it comes to ChIPSeq or DNA methylation (WGBS), either they ignore the issue all together and just use the existing methods for sequence alignment (like bowtie2 etc) or they have used other targeted PCR based methods for these types of data. I am aware that these targeted methods might be better options when it comes to these complex regions but now I have the data and I have to process and analyze it. Any idea how to proceed with my ChIPSeq and WGBS data for these regions?

Thank you very much in advance.

Cheers