Human-Mouse specific Conservation tracks?

[Awais Choudhry]

To whom it concerns,

Hi, my name is Awais, I am a student at the University of Adelaide, and I am writing to you because I am having difficulty finding where you store individual conservation tracks. I cannot find the track for human to mouse conservation scores. I have searched through the database extensively but it I am unable to find it. 

I maybe expecting the wrong format but, my understanding was there would be a .wig file which I could download that contains the conservation scores between human and mouse. 

Thank you in advance, and apologies for any inconvenience!

regards,

Awais

[Matthew Speir]

Hi Awais,

Thank you for your question about Human/Mouse conservation scores.

We don't produce conservation scores for pairwise alignments. See this answer to a previous mailing list question for a more detailed explanation: https://groups.google.com/a/soe.ucsc.edu/forum/#!msg/genome/LllcgG0uVFg/bAKu5OOEDAAJ.

Additionally, you may be able to use our "Net" tracks to look for homologous regions in the genome. You can find the Mouse (mm10) Chain/Net tracks for the human assembly hg38 in the Genome Browser here: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=placentalChainNet. You can also find the data for these pairwise alignments in a variety of formats here: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/vsMm10/. A description of the Net format is here: https://genome.ucsc.edu/goldenPath/help/net.html, and descriptions of other alignment formats, such as AXT or MAF, can be found here: https://genome.ucsc.edu/FAQ/FAQformat.html.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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