[request?] mitochondrial chromosomes

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Caleb Lareau created an issue

Hi Michael,

The new manuscript describing the tool is really fantastic-- I really enjoyed reading this. I've been concerned about mitochondrial genome contamination in some specific regions of the genome (and vice-versa). Is there an obvious way to include these in the genome builds or a reason why they were excluded?

Comments (2)

  1. Mehran Karimzadeh

    Hi Caleb,

    You can run Umap to generate mappability files of any genome, including the human genomes with mitochondrial chromosomes and unplaced contigs. For untargeted whole genome assays, of course, using an assembly with mitochondrial chromosome and unplaced contigs works better.

    There are different reports on methylation states of the mitochondrial DNA (e.g. PMID:PMC5671948). For the purpose of the manuscript, therefore, we didn't use unplaced contigs or mitochondrial DNA.

    If you come across any issue generating mappability files of any genome using Umap and Bismap, do let us know.

    Best, Mehran

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