We downloaded the macaque rheMac10 genome72 (https://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/bigZips/rheMac10.fa.gz) and human NCBI RefSeq transcriptome annotation gtf file from the UCSC genome browser (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.ncbiRefSeq.gtf.gz). We used the UCSC liftOver tool with the hg38toRheMac10 chain file (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToRheMac10.over.chain.gz) to overlay the human transcriptome gtf file onto the rheMac10 genome, with a minimal match threshold of 0.85. The human “liftOver” annotations were used to extend and supplement the macaque annotations, leading to greater numbers of genes called (Figure S1B).
