Hello,
I was wondering if you had any experience testing GSAlign with whole exome data for intra-species comparison purposes. For example, in one of your evaluations in the preprint you aligned the chimpanzee genome to the human genome. Would it be possible to align a chimpanzee exome to GRCh38 genome? Or similarly, perhaps a user has a series of mouse whole exome data and want to align it to a different mouse species genome.
My sense was that it may work for long exons, but perhaps may struggle with shorter sequences? I'm guessing at very least the -alen parameter would need to be reduced.
Thanks for any insights you can offer!
Hello, I was wondering if you had any experience testing GSAlign with whole exome data for intra-species comparison purposes. For example, in one of your evaluations in the preprint you aligned the chimpanzee genome to the human genome. Would it be possible to align a chimpanzee exome to GRCh38 genome? Or similarly, perhaps a user has a series of mouse whole exome data and want to align it to a different mouse species genome. My sense was that it may work for long exons, but perhaps may struggle with shorter sequences? I'm guessing at very least the
-alenparameter would need to be reduced. Thanks for any insights you can offer!