Annotation files for mHapTools

In order to run the whole workflow of DNA methylation haplotype analysis, some annotation files are needed. For example, genome files are required to align sequence reads using Bsmap; while Bismark indexes are required for Bismark alignment. CpG sites and indexes are specifically required to run mHapTools. These annotation files are hosted in our server and can also be accessed below.

For Human and Mouse

Genome	Reference	Bismark index	CpG sites	CpG Islands
hg19	hg19.fa	hg19_index	hg19_CpG.gz hg19_CpG.gz.tbi	hg19_cpgisland.bed
hg38	hg38.fa	hg38_index	hg38_CpG.gz hg38_CpG.gz.tbi	hg38_cpgisland.bed
mm9	mm9.fa	mm9_index	mm9_CpG.gz mm9_CpG.gz.tbi	mm9_cpgisland.bed
mm10	mm10.fa	mm10_index	mm10_CpG.gz mm10_CpG.gz.tbi	mm10_cpgisland.bed

For other genomes

If you are working with other genomes, you can let us konw and we will add more annotation files in the future. Alternatively, you can generate them as described below.