Using the 27-primates UCSC Multiz Alignment
Hello,
I am attempting to use the 27-primates UCSC multiz alignment data so that I can find an orthogonal sequence (across different mammals) to a human reference sequence (whether an ORF, a transcript, etc). I downloaded all the data in the maf folders here hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz30way/maf/, but am very lost on how to extract anything meaningful out of it. Specifically, even with its description, I am unclear on what the alignments and maf folders are, and how to read the files within them. If anyone could send a resources/explanations, it would be greatly appreciated. Thanks!
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