Appendix B — Supported genomes
EpiNexus 1.2 knows the 17 reference genomes in Table B.1. Each EpiNexus service installs the ones its users need; the New Project form and the run wizard list only the installed ones (Chapter 4). If your genome is not in the list, ask the EpiNexus team.
All genomes use chromosome names that start with “chr” (chr1, chr2, …, chrM). The DNA sequence comes from the UCSC Genome Browser, except for Arabidopsis, which comes from Ensembl Plants. For human, EpiNexus uses UCSC’s “analysis set”, which leaves out the alternative copies of some regions so that reads are not split between them (Chapter 3).
| Genome | Species | Gene annotation | Blacklist | JASPAR motifs |
|---|---|---|---|---|
| hg38 (GRCh38) | Human | GENCODE v46 | ENCODE unified GRCh38 exclusion list | vertebrates |
| hg19 (GRCh37) | Human | GENCODE v46lift37 | ENCODE Blacklist v2 | vertebrates |
| mm39 (GRCm39) | Mouse | GENCODE vM35 | excluderanges mm39 list | vertebrates |
| mm10 (GRCm38) | Mouse | GENCODE vM25 | ENCODE Blacklist v2 | vertebrates |
| rn7 (mRatBN7.2) | Rat | UCSC ncbiRefSeq | — | vertebrates |
| rn6 | Rat | UCSC ncbiRefSeq | — | vertebrates |
| dm6 (BDGP6) | Fruit fly | UCSC ncbiRefSeq | ENCODE Blacklist v2 | insects |
| danRer11 (GRCz11) | Zebrafish | UCSC ncbiRefSeq | — | vertebrates |
| ce11 (WBcel235) | C. elegans | UCSC ncbiRefSeq | ENCODE Blacklist v2 | nematodes |
| sacCer3 (R64) | Yeast | UCSC ncbiRefSeq | — | fungi |
| galGal6 (GRCg6a) | Chicken | UCSC ncbiRefSeq | — | vertebrates |
| rheMac10 (Mmul_10) | Macaque | UCSC ncbiRefSeq | — | vertebrates |
| susScr11 (Sscrofa11.1) | Pig | UCSC ncbiRefSeq | — | vertebrates |
| bosTau9 (ARS-UCD1.2) | Cow | UCSC ncbiRefSeq | — | vertebrates |
| canFam6 (UU_Cfam_GSD_1.0) | Dog | UCSC ncbiRefSeq | — | vertebrates |
| xenLae2 (v10.1) | Frog (X. laevis) | UCSC ncbiRefSeq | — | vertebrates |
| tair10 | Arabidopsis | Ensembl Plants 62 | excluderanges TAIR10 list (Klasfeld, 20 inputs) | plants |
Notes:
- Blacklists remove regions that collect reads in every experiment (Chapter 3). A dash means that no published list exists for the genome; peaks there are not filtered, and EpiNexus says so in the run’s warnings. The lists come from ENCODE and the Boyle lab (Amemiya et al. 2019) or from the excluderanges collection.
- Organelles. ATAC-seq reads on the mitochondrial genome (chrM) are removed. For Arabidopsis, the chloroplast genome (chrC) is removed too.
- Gene Ontology annotations come from NCBI for each species (Chapter 11).
- Bisulfite (DNA methylation) analysis needs an extra index for each genome. Ask the EpiNexus team which genomes have one.