README.md

Ensembl BioMart

• Go to Ensembl portal and select BioMart
  • Human GRCh37: https://grch37.ensembl.org/
  • All others: http://ensembl.org/
• Select the following attributes:
  • Chromosome/scaffold name
  • Gene start (bp)
  • Gene end (bp)
  • Gene stable ID
  • Gene stable ID version
  • Gene name
  • Gene type
• Export the results to a tsv file.
• Sort them:
  • cat mart_export.txt | awk 'NR==1' > EnsemblBioMart.GRCh37p13.EnsemblGenes104.tsv
  • cat mart_export.txt | awk 'NR>1' | sort -k1,1V -k2,2n -k3,3n >> EnsemblBioMart.GRCh37p13.EnsemblGenes104.tsv
• Edit the header line:
  • #Chromosome Gene_start Gene_end Gene_stable_ID Gene_stable_ID_version Gene_symbol Gene_type
• Compress and index them:
  • bgzip -l9 EnsemblBioMart.GRCh37p13.EnsemblGenes104.tsv
  • tabix -s1 -b2 -e3 EnsemblBioMart.GRCh37p13.EnsemblGenes104.tsv.gz