gtf2bed doesn't give gene_id in the bed file

Question

[Biologist]

I have a gtf sample.gtf like:

GL000009.2      ENSEMBL exon    56140   58376   .       -       .       transcript_id "transc_00000026"; gene_id "ENSG00000278704.1"; gene_name "ENSG00000278704.1"; exon_number "1"; inf "known"; true_gene_id "XLOC_000032";
GL000009.2      ENSEMBL transcript      56140   58376   .       -       .       transcript_id "transc_00000026"; gene_id "ENSG00000278704.1"; gene_name "ENSG00000278704.1"; oId "ENST00000618686.1"; tss_id "TSS35"; inf "known"; true_gene_id "XLOC_000032";
GL000009.2      Cufflinks       exon    59669   59932   .       +       .       transcript_id "transc_00000028"; gene_id "XLOC_000023"; gene_name "XLOC_000023"; exon_number "1"; inf "unknown"; true_gene_id "XLOC_000023";
GL000009.2      Cufflinks       transcript      59669   61563   .       +       .       transcript_id "transc_00000028"; gene_id "XLOC_000023"; gene_name "XLOC_000023"; oId "TCONS_00000027"; class_code "u"; tss_id "TSS25"; inf "unknown"; true_gene_id "XLOC_000023";

I converted gtf to bed using gtf2bed

gtf2bed < sample.gtf > sample.bed

And the bed file looks like:

GL000009.2      56139   58376   XLOC_000032     .       -       ENSEMBL exon    .       transcript_id "transc_00000026"; gene_id "ENSG00000278704.1"; gene_name "ENSG00000278704.1"; exon_number "1"; inf "known"; true_gene_id "XLOC_000032";
GL000009.2      56139   58376   XLOC_000032     .       -       ENSEMBL transcript      .       transcript_id "transc_00000026"; gene_id "ENSG00000278704.1"; gene_name "ENSG00000278704.1"; oId "ENST00000618686.1"; tss_id "TSS35"; inf "known"; true_gene_id "XLOC_000032";
GL000009.2      59668   59932   XLOC_000023     .       +       Cufflinks       exon    .       transcript_id "transc_00000028"; gene_id "XLOC_000023"; gene_name "XLOC_000023"; exon_number "1"; inf "unknown"; true_gene_id "XLOC_000023";
GL000009.2      59668   61563   XLOC_000023     .       +       Cufflinks       transcript      .       transcript_id "transc_00000028"; gene_id "XLOC_000023"; gene_name "XLOC_000023"; oId "TCONS_00000027"; class_code "u"; tss_id "TSS25"; inf "unknown"; true_gene_id "XLOC_000023";

Why is the 4th column in the bed file, not gene_id? It looks like it is taking true_gene_id. I want the output to be like below:

GL000009.2      56139   58376   ENSG00000278704.1     .       -       ENSEMBL exon    .       transcript_id "transc_00000026"; gene_id "ENSG00000278704.1"; gene_name "ENSG00000278704.1"; exon_number "1"; inf "known"; true_gene_id "XLOC_000032";
GL000009.2      56139   58376   ENSG00000278704.1     .       -       ENSEMBL transcript      .       transcript_id "transc_00000026"; gene_id "ENSG00000278704.1"; gene_name "ENSG00000278704.1"; oId "ENST00000618686.1"; tss_id "TSS35"; inf "known"; true_gene_id "XLOC_000032";
GL000009.2      59668   59932   XLOC_000023     .       +       Cufflinks       exon    .       transcript_id "transc_00000028"; gene_id "XLOC_000023"; gene_name "XLOC_000023"; exon_number "1"; inf "unknown"; true_gene_id "XLOC_000023";
GL000009.2      59668   61563   XLOC_000023     .       +       Cufflinks       transcript      .       transcript_id "transc_00000028"; gene_id "XLOC_000023"; gene_name "XLOC_000023"; oId "TCONS_00000027"; class_code "u"; tss_id "TSS25"; inf "unknown"; true_gene_id "XLOC_000023";

How to get the desired output?

[stolarek.ir]

I got a bit frustrated with gtf2bed and started using GTFtools python package:

http://www.genemine.org/gtftools.php

Answer 1

[ATpoint]

That's odd. Are you using the latest version? Try adding --attribute-key=gene_id.

[Biologist]

Do you mean like this?

gtf2bed --attribute-key=gene_id < sample.gtf > sample.bed

I'm using the version: 2.4.39