Reference Files

Genome Reference

The 4DN Data Portal currently hosts the genome references of 5 species - human, mouse, chicken, fruit fly and zebrafish, in various formats. The reference genomes of human and mouse are identical to those used by the ENCODE consortium.

species	genome version	fasta	BWA index	Bowtie2 index
human	GRCh38 no alt v15 (encode)	fasta.gz	tgz / tar	tar
mouse	mm10/GRCm38 no alt (encode)	fasta.gz	tgz / tar	tar
chicken	galGal5	fasta.gz	tgz
fruit fly	dm6	fasta.gz	tgz
zebrafish	danRer11/GRCz11	fasta.gz	tgz

Chrom Sizes

Chrom sizes files in the following tab-delimited text format are also hosted. Main-only chrom sizes files contain only chromosomes and not contigs.

<chr_1>  <length_of_chr_2>
<chr_2>  <length_of_chr_2>
...

Chrom Sizes by Species
species	chrom sizes
human	main only / all
mouse	main only / all
chicken	main only / extended
fruit fly	main only
zebrafish	main only

Gene Annotation

Consistent with ENCODE, we host gene annotations for human and mouse based on GENCODE. All data processing at the portal involving gene annotations uses these annotation files.

species	annotation version	GTF/GFF	transcript-gene mapping	Star index	RSEM index	HiGlass
human	GENCODE V29	encode	tsv	tgz	tgz	beddb
mouse	GENCODE M21	encode	tsv	tgz	tgz	beddb

Restriction Enzyme Sites

The genomic positions of restriction enzyme sites are listed in the following format that the Juicer program recognizes.

<chr_1> <position_1> <position_2> <position_3> ... <chr_2> <position_1> <position_2> <position_3> ... ...

An example of a few fields in the first line looks as below:

chr1 3004105 3005820 3008316 3008894 3009813

The files can be obtained from the links below.

species	HindIII	MboI	DpnII	NcoI	MspI	NcoI-MspI-BspHI mix	AluI	DdeI	DdeI-DpnII mix
human	txt	txt	txt	txt	txt	txt	txt	txt	txt
mouse	txt	txt	txt
chicken	txt
fruit fly		txt
zebrafish		txt