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:
GCF_002263795.1_ARS-UCD1.2_refseq_chrids.fa.gz
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.
GCF_002263795.1_ARS-UCD1.2_with_y_refseq_chrids.fa.gz
The NCBI gene annotation gff3 file were parsed into three files, excluding pseudogenes:
ARS-UCD1.2_RefSeq_all_proteincoding.gff3.gz
ARS-UCD1.2_RefSeq_all_lncRNA.gff3.gz
ARS-UCD1.2_RefSeq_other_rna.gff3.gz
The gff3 have been converted to gtf for use with Hisat2, StringTie, and read count tools:
ARS-UCD1.2_RefSeq_all_proteincoding_with_symbol.gtf.gz
ARS-UCD1.2_RefSeq_all_lncRNA_with_symbol.gtf.gz
ARS-UCD1.2_RefSeq_other_rna_with_symbol.gtf.gz