Where to get Gene start position to end positon for all gene in an organism

Question

[Bioblazer]

In a transcript file (.gtf) we can able to get exon wise start position and stop position, CDS and start codon region and stop codon region,but I want start position and end position of all genes (not exon wise) with its chromosome number in an organism.

Answer 1

[Devon Ryan]

Normally there's a "gene" entry for each gene, so:

awk 'BEGIN{FS="\t"; OFS="\t"}{if($3 == "gene") print $1, $4, $5}' foo.gtf

[Bioblazer]

Thank you very much for your kind reply

Answer 2

[EagleEye]

As Devon said if the GTF file is from Gencode, you will have "gene" entry. Extracting "gene" entry will give you the desired results. If you use Ensembl GTF annotation (hg19 upto GRCh37.74), it does not have "gene" entry. In this case use the following script.

The output will look similar to

[Bioblazer]

Thank you so much for your valuable reply.

[rek89]

Hello, I have this exact same question but I'm not seeing the code here. Anyway you could please resend the code?

[EagleEye]

How do I get the gene annotation for the latest version (GRCh38)?