Recently I read a paper named " Identification of constrained sequence elements across 239 primate genomes", which provide 239 primate species whole-genome multiple sequence alignment file.
I want to download this MSA file. In data availability section, it's said "The MSA and constraint tracks are available through the UCSC Genome Browser", but I failed to find the way to download this file from UCSC genome browser. I have only downloaded sone genome data from this website before, and I'm not sure how to download article publication data from it.
I have emailed the author of the article to inquire, but have not received a reply yet
Thanks a lot for any advice!
This is likely the track for the alignments: https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=1864082160_DDnWFQjynpPghw7Dk1YwIpTLDIV9&db=hg38&c=chr2&g=cons241way
You will need to turn this track on full.
You can download the MAF/PhyloSeq files from: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus241way/
Thanks a lot for replying ! I know this data, and it's from another paper published by zoonomia project.
It seems that my data source article integrated 239 primates with this data, finally producing the 447-way alignment result. Maybe they only release the integrated file. I'll try to remove non-primate genome from 447-way alignment to get pure primate MAF file.
Thank you once again for your response ^_^