Reference Sequences

Genome References

The ENCODE project uses Reference Genomes from NCBI or UCSC to provide a consistent framework for mapping high-throughput sequencing data. In general, ENCODE data are mapped consistently to 2 human (GRCH38, hg19) and 2 mouse (mm9/mm10) genomes for historical comparability. Drosophia melanogaster experiments are mapped to either dm3 or dm6 and Caenorhabdilis elegans experiments are mapped to ce10 or ce11. The official reference files for each Uniform processing pipeline can be found in the table below, organized by organism and pipeline. In addition to the genome sequences (we generally use the "no alt" version for each genome), a variety of other crucial files can be found there as well (GENCODE transcript references, chromosome size files, the phage lambda genome, etc.).

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Reference File Sets 

The table below includes files used by each pipeline for uniform processing by the ENCODE DCC, with associated details on genome assembly and annotation, if applicable.  For your convenience, the GRC genome assembly and GENCODE annotation files are directly linked below. For further information, please contact encode-help@lists.stanford.edu

ENCODE4 Uniform Processing Pipeline Filesets

Organism	Pipeline(s)	Reference file set	Genome assembly & annotation
	ATAC-seq	ENCSR938RZZ	GRCh38 with GENCODE version V29
	Bulk RNA-seq	ENCSR151GDH	GRCh38 with GENCODE version V29
	ChIP-seq	ENCSR174MOP (TF, Histone)	GRCh38
		ENCSR487FYI (MINT-ChIP)	GRCh38
	DNase-seq	ENCSR083JOX	GRCh38
	Long read RNA-seq	ENCSR925QOG	GRCh38 with GENCODE version V29
	microRNA-seq	ENCSR608ULQ	GRCh38 with GENCODE version V29
	WGBS	ENCSR475CAG	GRCh38
	ATAC-seq	ENCSR535HHO	mm10 with GENCODE version M21
	Bulk RNA-seq	ENCSR496QMW	mm10 with GENCODE version M21
	ChIP-seq	ENCSR928IAF (TF, Histone)	mm10
		ENCSR879BNV (MINT-ChIP)	mm10
	DNase-seq	ENCSR029SEE	mm10
	Long read RNA-seq	ENCSR069LTV	mm10 with GENCODE version M21
	microRNA-seq	ENCSR536KRM	mm10 with GENCODEversion M21
	WGBS	ENCSR923XUC	mm10

 

Genome assemblies:

Reference File	Description
GRCh38_no_alt_analysis_set_GCA_000001405.15 [download]	GRCh38 XY reference genome (ENCODE3 used only one reference genome for analysis)
female.hg19 [download]	hg19 XX reference genome (ENCODE2 used sex-specific genomes for analysis)
male.hg19 [download]	hg19 XY reference genome (ENCODE2 used sex-specific genomes for analysis)
mm10_no_alt_analysis_set_ENCODE [download]	mm10 XY reference genome (ENCODE3 used only one reference genome for analysis)
female.mm10 [download]	XX mm10 "minimal", which has been replaced by mm10_no_alt_analysis_set_ENCODE.fasta
male.mm10 [download]	XY mm10 "minimal", which has been replaced by mm10_no_alt_analysis_set_ENCODE.fasta

 

Genome annotations:

Reference File	Description
ENCFF159KBI [download]	GRCh38 GENCODE V29 merged annotations gtf file
ENCFF824ZKD [download] & ENCFF316JQJ [download]	GRCh38 GENCODE V24 gtf and tar files
gencode.v19.annotation [download]	hg19 GENCODE V19 gtf file
ENCFF871VGR [download]	mm10 GENCODE VM21 merged annotations gtf file
gencode.vM7.annotation [download]	mm10 GENCODE M7 gtf file
gencode.vM4.annotation [download]	mm10 GENCODE M4 gtf file

 

Additional useful files for uniform processing pipelines:

Reference File	Description
ENCFF908UQN [download]	spike-in sequence used for RNA-seq analysis
lambda.fa [download]	phage λ wild type assembly J02459.1 (used as a methylation negative control)
ENCFF356LFX [download]	ChIP GRCh38 blacklist
ENCFF200UUD [download]	MINT-ChIP hg19 blacklist
ENCFF023CZC [download]	MINT-ChIP GRCh38 blacklist

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Collection of References

Some of the experiments at the ENCODE portal have not been processed by the DCC uniform processing pipelines and may have used different reference files. The References search page includes all the reference datasets used by the different projects whose data could be found on the portal.

Updated January 05, 2021