The genome assembly and gene annotation data were downloaded from the NCBI ftp site:
For BovineMine and JBrowse we converted chromosome identifiers to numbers and letters (1-29, MT, X), but kept RefSeq accessions for unassigned scaffolds:
The following file is the ARS-UCD1.2 genome assembly with the Y chromosome added from the Btau_5.1 assembly, which is used in BGD BLAST.
The NCBI gene annotation gff3 file were parsed into three files, excluding pseudogenes:
The gff3 have been converted to gtf for use with Hisat2, StringTie, and read count tools:
The following is a liftover chain file that can be used to transfer feature coordinates from UMD3.1.1 to ARS-UCD1.2. We used this file to create the dbSNP and alternate assembly tracks for ARS-UCD1.2 JBrowse. The identifiers used in this chain file for UMD3.1.1 are from GenBank (e.g. GK000001.2, GJ058435.1). The identifiers used for ARS-UCD1.2 are those described above (1-29, X, MT, RefSeq scaffold accessions). Please contact the BGD site admin if you need different identifiers.