Genomic regions

Genomic regions annotations generated by BBGLab Data includes:

• 3utr
• introns
• mirna_mat
• tfbs
• 5utr
• lncrna_distal_promoters
• mirna_pre
• utr
• cds
• lncrna_exons
• other_ncrnas
• distal_promoters
• lncrna_proximal_promoters
• proximal_promoters
• enhancer
• lncrna_splice_sites
• splice_sites

Releases

• Release 2 (30-09-2020): The coordinates are extracted from the gtf3 annotation file.

  • CDS coordinates are generated in two flavours: with and without (default) STOP codon.
  • Gencode v35
  • Ensembl canonical transcripts v101

• Release 1 (2019): The coordinates are extracted from the gtf annotation file.

  • CDS coordinates are generated without STOP codon.
  • Gencode v31
  • Ensembl canonical transcripts v97

Description

You can find the data in the folder: /workspace/projects/genomic_regions/

• ./raw_data: contains databases from which raw data has been downloaded
• ./scripts: contains code to parse raw data
• ./hg19: contains genomic annotations in hg19 reference genome
• ./hg38: contains genomic annotations in hg38 reference genome

Reference

• Joan Enric

Created on 2019-07-08 by claudia.arnedo@irbbarcelona.org