GENCODE v.27 BED 12 file

Question

[samuel]

Hi, Does anyone know where you can get a BED 12 format file of the latest version of GENCODE? I have tried this link which didn't work: https://github.com/stevekm/reference-annotations

I need the bed 12 format so this doesn't work either:

cat gencode.v27.gtf | awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],".",$7}' | sed 's/gene_id //g' | tr -d '"' > file.bed

Many thanks.

[GenoMax]

You can make a BED12 file extending your command above. Problem is the fields downstream are fixed values derived from the BED6. What are you planning to use this BED12 file for?

cat gencode.v27.gtf | awk 'BEGIN{FS="\t";OFS="\t"}{if($1 ~ /^ch/){split($9,a,";");print $1,$4-1,$5,a[1],"0",$7,$4-1,$4-1,"255,0,0",1,$5-$4,$4-1}else{print $0}}' | sed 's/gene_id //g' | tr -d '"' > file.bed

Answer 1

[michael.ante]

Hi zoegward,

I used once the gtf2bed.pl program from the ea-utils. As far as I remember, it creates for each transcript a line in the resulting bed file. Thereby, it describes the transcripts' exon-usage, while loosing the transcript-gene association.

On the other hand, a GTF file implements the gene - transcript - exon relationships in an hierarchical way. This leads to a lot of redundant information.

Cheers,

Michael