Create NCBI RefSeq Select BED12 file

ncbi_refseq_select_bed12.md

Create NCBI RefSeq Select BED12 file

This gist shows you how to create a BED file in BED12 format containing every protein-coding NCBI RefSeq Select gene with the exons annotated as blocks in the BED file.

1. First, download a TSV file of NCBI RefSeq Select genes

   1. Go to the UCSC Table Browser
   2. Select these parameters
      • Assembly: Dec. 2013 (GRCh38/hg38)
      • Group: Genes and Gene Predictions
      • Track: NCBI RefSeq
      • Table: RefSeq Select and MANE (ncbiRefSeqSelect)
      • Output format: all fields from selected table
      • Output filename: GRCh38.ncbiRefSeqSelect.tsv.gz
      • File type returned: gzip compressed
   3. Click "get output"

2. Use the awk script below to process the TSV into BED12 format.

   zcat GRCh38.ncbiRefSeqSelect.tsv.gz \
     | tail -n +2 \
     | awk -f ncbi_refseq_tsv_to_exon_bed12.awk - \
     > GRCh38.ncbiRefSeqSelect.genes.bed

ncbi_refseq_tsv_to_exon_bed12.awk

BEGIN {
    IFS="\t"; OFS="\t";
}
{
    n=split($10, exon_starts, ",");
    split($11, exon_ends, ",");
    exon_sizes_str=exon_ends[1]-exon_starts[1];
    exon_starts_str=exon_starts[1];
    for (i=2; i<n; i++) {
        exon_sizes_str=exon_sizes_str","exon_ends[i]-exon_starts[i];
        exon_starts_str=exon_starts_str","exon_starts[i];
    };
    print $3,$5,$6,$13,0,$4,$7,$8,"33,33,33",$9,exon_sizes_str,exon_starts_str
}