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Unclear conversion extraction subsetting #307

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fgualdr opened this issue Oct 7, 2024 · 1 comment
Open

Unclear conversion extraction subsetting #307

fgualdr opened this issue Oct 7, 2024 · 1 comment

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@fgualdr
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fgualdr commented Oct 7, 2024

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

@glennhickey
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Please use taffy for subsetting and querying MAF files. It's included in the Cactus releases (binary or docker) if you don't want to build it yourself.

maf2hal doesn't scale very well and is used mostly for tests -- you are better off dealing directly with the MAF than converting to HAL.

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