Multiz for human-to-mouse and mouse-to-human don't agree with each other

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4.8 years ago

Eric Lim ★ 2.1k

I'm not entirely sure what this means and hoping the community can put me in the right direction.

In mouse (GRCm38/mm10), the sequence shows decent similarity as human (GRCh38/hg38) with a few mismatches.

Mouse to human multiz

In human (GRCh38/hg38), = is used.

Human to mouse multiz

This seems to only occur in GRCh38/hg38. GRCh37/hg19 shows the expected result.

Any idea what this means?

ucsc multiz • 1.1k views

ADD COMMENT • link updated 4.6 years ago by Biostar 20 • written 4.8 years ago by Eric Lim ★ 2.1k

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Hey Eric,

As genomax mentions, could you email this question to genome@soe.ucsc.edu?

Since your question is specifically related to GB generated data, it would be helpful if the whole team sees it. Also, if you could include the regions where the screenshots are taken from, as links or session links, that would also be helpful.

ADD REPLY • link 4.7 years ago by Luis Nassar ▴ 650

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Thanks Luis. I've asked one of my colleagues to look into this further and will make sure he emails the question to the mailing list.

ADD REPLY • link 4.7 years ago by Eric Lim ★ 2.1k

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Is this region from a gene? Have you checked Ensembl's compara to see what they predict?

ADD REPLY • link 4.8 years ago by GenoMax 141k

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Yeah, it's an annotated exon of a gene. I don't really know how to use compara, but my random clicking around seems like this region is aligned correctly in Emsembl.

ADD REPLY • link 4.8 years ago by Eric Lim ★ 2.1k

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So it may be useful to put a ticket in to UCSC genome browser support pointing out this issue.

ADD REPLY • link 4.8 years ago by GenoMax 141k

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