Questions regarding downloading flatfiles for Macaque

[Christina Mulch]

Greetings USCS, I work on a project that maintains a rhesus Macaque database at Oregon’s National Primate Center and I have been tasked with updating the annotation sources. I want to make sure I’m capturing the most complete files available for download from your resources to add into our variant annotation pipeline.

I’ve found that there are several ways to access data for download on the UCSC site, one being the table pull request and the other accesses the ftp sites.

 

https://genome.ucsc.edu/cgi-bin/hgTables

or alternatively accessing data through the ftp site:

https://genome.ucsc.edu/goldenPath/help/ftp.html

 

additionally, I am unclear about conservation data relative to the macaque genome? Can you download a complete flat file in human coordinates?

Any helpful information or guidance you can provide would be much appreciated.

Thanks and Best,

Christina Mulch

 

 

She/Her

Division of genetics

Computational Biologist

Oregon National Regional Primate Center

[Hiram Clawson]

Good Afternoon Christina:

Please note several different versions of the assemblies for Macaque
are available at UCSC.

2013 GCA_000364345.1 Macaca_fascicularis_5.0 WashU
http://hgdownload.soe.ucsc.edu/goldenPath/macFas5/
http://hgdownload.soe.ucsc.edu/goldenPath/macFas5/liftOver/

2020 GCA_011100615.1 Macaca_fascicularis_6.0 Baylor
https://hgdownload.soe.ucsc.edu/hubs/GCA/011/100/615/GCA_011100615.1/

2021 GCF_012559485.2 MFA1912RKSv2 Keio University
https://hgdownload.soe.ucsc.edu/hubs/GCF/012/559/485/GCF_012559485.2/
https://hgdownload.soe.ucsc.edu/hubs/GCF/012/559/485/GCF_012559485.2/liftOver/

The liftOver/ directories have over.chain.gz files to translate those
genomes to other genome assemblies.

--Hiram