GeneBEDs resources
GeneBED resources are transcript-level annotations. all contains every
transcript isoform; deduplong keeps one longest isoform per gene. The
def link points to the registry-defined default version.
Bundled GENCODE builds include hg19, hg38, mm9, mm10, and mm39.
Other assemblies are resolved from GENCODE, UCSC, or Ensembl.
Commands
sjcab-peak2anno-db install-genebed
sjcab-peak2anno-db install-genebed mm10 vM22 -g gencode.vM22.annotation.gtf.gz
sjcab-peak2anno-db download-genebed hg38 v31 -o annotations
sjcab-peak2anno-db download-genebed hg19 v31lift37 -o annotations
sjcab-peak2anno-db install-genebed hg38 -name human
For Ensembl, def, default, current, and latest resolve the current
release. Vertebrate and Ensembl Genomes catalogues are cached by release;
def links to the current release. Assembly, species, name, and
assembly_accession can be used as species identifiers when unique.
For UCSC builds, GTF metadata and liftOver chain URLs are cached in
{db-path}/ucsc/gtf_builds.tsv. Sizes files use the assembly name whenever
possible; .sizes.clean uses primary chromosomes from the assembly report.
Use -name with install-genebed to store a selected GeneBED set under a
custom species name; the mapping is recorded in custom.name.tsv.
Layout
{db-path}/genebed/{species}/{version}/all.gene.bed
{db-path}/genebed/{species}/{version}/deduplong.gene.bed
{db-path}/genebed/{species}/def -> {version}
{db-path}/sizes/{species}.sizes
{db-path}/sizes/{species}.sizes.clean
GeneBED generation from a local GTF
sjcab-peak2anno-db download-genebed mm10 vM22 \
--gtf-path gencode.vM22.annotation.gtf.gz \
--output-dir annotations
Use --gene-type repeatedly to restrict GENCODE types. See
FeatureBEDs for derived regions and
Deduplication for transcript selection.
GTF resolution URLs
The resolver checks these sources for the GTF associated with a GeneBED: