Galaxy |

Retrieve Ensembl features in BED format (version 0.1.0)

Ensembl species:

Keep extra columns from ensembl BED:

Use the UCSC names for Chromosomes:

Restrict Feature retrieval to these biotypes:

Example biotypes: protein_coding, non_coding, pseudogene, nonsense_mediated_decay, non_stop_decay, translated_processed_pseudogene, transcribed_processed_pseudogene, transcribed_unitary_pseudogene, transcribed_unprocessed_pseudogene, polymorphic_pseudogene, processed_pseudogene, unprocessed_pseudogene, unitary_pseudogene, processed_transcript, retained_intron, ccds_gene, sense_overlapping, sense_intronic, cdna_update, antisense, LRG_gene, IG_C_gene, IG_D_gene, IG_J_gene, IG_LV_gene IG_V_gene, TR_C_gene, TR_D_gene, TR_J_gene, TR_V_gene, IG_pseudogene, IG_C_pseudogene, IG_D_pseudogene, IG_J_pseudogene, IG_V_pseudogene, TR_J_pseudogene, TR_V_pseudogene, TEC, ribozyme, RNase_P_RNA, guide_RNA, macro_lncRNA, bidirectional_promoter_lncRNA, 3prime_overlapping_ncRNA, antisense_RNA, vaultRNA, Y_RNA, SRP_RNA, RNase_MRP_RNA, IG_C_pseudogene, lncRNA, lincRNA, miRNA, snRNA, sRNA, telomerase_RNA, Mt_tRNA, Mt_rRNA, scaRNA, misc_RNA, rRNA, tRNA, scRNA, snoRNA, other

Restrict Feature retrieval to comma-separated list of regions:

Each region is specifed as: chr or chr:pos or chr:from-to

Retrieve the intervals from this file:

Retrieve Ensembl cDNAs in BED format

usage: retrieve_ensembl_bed.py [-h] [-s SPECIES] [-R REGIONS] [-B BIOTYPES]

[-X] [-U] [-t] [-v] [-d] output

positional arguments:

output Output BED filepath, or for stdout: "-"

optional arguments:

`-h, --help`	show this help message and exit
`-s SPECIES, --species SPECIES`
	Ensembl Species to retrieve
`-R REGIONS, --regions REGIONS`
	Restrict Ensembl retrieval to regions e.g. X,2:20000-25000,3:100-500+
`-i INTERVAL_FILE, --interval_file INTERVAL_FILE`
	Regions from a bed, gff, or interval file

-f {bed,gff,interval}, --interval_format {bed,gff,interval}: Interval format has TAB-separated columns: Seq, Start, End, Strand

`-B BIOTYPES, --biotypes BIOTYPES`
	Restrict Ensembl biotypes to retrieve
`-X, --extended_bed`
	Include the extended columns returned from Ensembl
`-U, --ucsc_chrom_names`
	Use the UCSC names for Chromosomes
`-t, --toplevel`	Print Ensembl toplevel for species
`-v, --verbose`	Verbose
`-d, --debug`	Debug

Output

Ensembl REST API returns an extended BED format with these additional columns:

second_name, cds_start_status, cds_end_status, exon_frames, type, gene_name, second_gene_name, gene_type