Rhesus Macaque - updated Reference

[Simon Deycmar]

Dear IGV Team,

I was looking for genes in rhesus macaques but the previous RheMac8 misses some gene annotations (such as Neurog1, Sox1, etc.).   There is a more recent reference genome Mmul_10 (https://www.ncbi.nlm.nih.gov/assembly/GCF_003339765.1/ ) which has less gaps and I guess also a more complete annotation. It would be great if you could add this to the IGV hosted genomes. 

Thank you a lot for your efforts,

Simon

[James Robinson]

OK this is done. Data, as usual,  downloaded from UCSC https://hgdownload.soe.ucsc.edu/downloads.html#rhesus

[Simon Deycmar]

Thank you a lot for your efforts !!   I really appreciate your input and wish you a great evening ! 

[David O'Connor]

Hi there --

Resurrecting a four year old thread because I was looking for the Mmul10 genome in the hosted genomes and could not find it there. I was able to load it from GenArk, but this has a limitation: gene names do not autocomplete, which makes browsing more difficult. I was able to download a GTF annotation file and load it as a track, which allowed autocompletion to work intermittently. Is it possible to restore Mmul10 as an IGV-hosted genome that supports autocompletion out of the box?

Thanks,

Dave

[James Robinson]

Hi Dave,

We are no longer hosting genomes ourselves,  some legacy genomes remain but are being phased out over time in favor of the UCSC hosted files.   Perhaps we could get autocompletion to work with those genomes but it's not immediately obvious how.   In the meantime your solution is probably the best one.