How to download article publication data from UCSC genome browser

Question

[Yurun]

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!

[GenoMax]

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/

[Yurun]

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 ^_^

Answer 1

[nullmodel]

You can find this alignment in the 'Cactus 447way' track: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=cons447way

Maf file download available: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus447way/

[GenoMax]

Just a note, 447-way alignment includes organisms besides the primates. OP was asking about primates specifically.

[nullmodel]

The Cactus 447-way alignment contains the referenced 239 primate genomes. There is no specific track by itself that has the 239 primate genomes. The zoonomia 241-way alignment is a much older project that also happens to be included in this 447-way alignment.

[GenoMax]

The zoonomia 241-way alignment is a much older project

I will move my answer to a comment in light of that. OP seemed to indicate that the paper they read made it sound like this information was available via UCSC. Perhaps it was an older paper they read for the data I had linked above.

[Yurun]

Thank you very much for the link! This helps me a lot. Exactly as GenoMax said I wanted pure primates MAF file, but I believe I could do some processing on this file to get it. Really appreciate your assistance ^_^