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Unclear conversion extraction subsetting #307

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@fgualdr

Hi,
I am trying to use available MAF files from UCSC (by chromosomes) to extract some information.
It is unclear to me what I should do to:

  • change the root (I am working with the hg38 100-way vertebrate) from human to mouse
  • Extract sub-groups (i.e. rodent, glides etc.. once I changed the root)
  • Use the extracted groups to generate conservation tracks.

I though I should use the maf2hal with the --refGenome mm10 for each chromosomes and then the halExtract listing the names but I am having issues.

Thanks for the help

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