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