ARS-UCD1.2 Downloads

The genome assembly and gene annotation data were downloaded from the NCBI ftp site:

ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Bos_taurus/latest_assembly_versions/GCF_002263795.1_ARS-UCD1.2/

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

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.

UMD3.1.1_to_ARS-UCD1.2_liftover.chn.gz