Human centromeres are located at repetitive alpha satellite DNA arrays that compose approximately 5% of the genome. Is this the reason why we can't find methylation info in centromeres?
Refer the paper "Human DNA methylomes at base resolution show widespread epigenomic differences", the Fig 1 d shows the human DNA methylomes in chromosome 12, the black rectangle is where the centromere located. So, how to understand this?
You'll only get multimappers in those regions and you typically ignore multimappers when determining methylation.
What you mean that it is the reason of mapper (like Bismark) which didn't map to the centromere? CpGi existed centromere area?
Bismark et al. can map there, but when a methylation extractor (either bismark's or a different one) is run on the alignment results it'll normally skip multimappers. I haven't a clue if there are any CpG islands in the centromere, I've never looked.
I see. Thank you so much for your prompt answer! That's very appreciated!
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if you will lay your hands on dataset from illumina moleculo, you will get near perfect >1 kb reads spanning centromeres from both ends. Beside that you could also look into data from 10X <- it's also a sequencing done in a limited space and then assembled and given to you as reads