Hello all,
I am having a supremely annoying time finding an appropriate annotation file for RheMac2. This is my first time doing this. I am doing a featurecount on RNA data. I used RheMac2 to align the reads with BWA-MEM through galaxy. However, I need help finding a file (GTF, GFF, or SAF) for an actual annotation for RheMac2. I see people reference it but can't seem actually to locate it. I tried using Liftover with rhemac8 to rhemac2, and while it kind of works, some genes are lost in the process. I think it is ridiculous that I can not find a simple annotation file for RheMac2, which pretty clearly exists. If anyone could point me to a precise link to download it that would be so appreciated. I am aware that I am most likely being incredibly stupid.
Where did you get the reference genomes from originally? It is best to get annotations from the same source. This looks like a very old genome release so you may be best off using the latest genome build which is (Mmul_10).
That said Rhesus macaque (Macaca mulatta) latest genome/annotation can be found at NCBI here: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_003339765.1/ Click on the
Downloadbutton and then select the reference and matching annotation files.Ensembl's version of the reference and annotations can be download here: http://useast.ensembl.org/Macaca_mulatta/Info/Index
RheMac2 genome can be found under
other genomeshere: https://hgdownload.soe.ucsc.edu/downloads.html