Question

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

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7.9 years ago

Bioblazer ▴ 50

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.

gene genome • 5.2k views

ADD COMMENT • link updated 2.9 years ago by EagleEye 7.5k • written 7.9 years ago by Bioblazer ▴ 50

score 3 · Answer 1 · 2016-06-06

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7.9 years ago

Devon Ryan 104k

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

ADD COMMENT • link 7.9 years ago by Devon Ryan 104k

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Thank you very much for your kind reply

ADD REPLY • link 7.9 years ago by Bioblazer ▴ 50

score 2 · Answer 2 · 2016-06-06

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7.9 years ago

EagleEye 7.5k

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

enter image description here

ADD COMMENT • link 7.9 years ago by EagleEye 7.5k

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Thank you so much for your valuable reply.

ADD REPLY • link 7.9 years ago by Bioblazer ▴ 50

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