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count protein-coding genes per contig

Hi everyone,

Any idea on how to count protein-coding genes only per contig/scaffold/chr?

Thanks, Diego

number protein-coding contig genes genome
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updated by iraun iraun • written by Diego • Diego

1 answer

If you have an annotation file, as for example, the following GTF from human:

1   havana  gene    11869   14409   .   +   .   gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
1   havana  transcript  11869   14409   .   +   .   gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; tag "basic"; transcript_support_level "1";

You could get the number of protein coding genes per chromosome using:

awk '$3=="gene"' Homo_sapiens.GRCh38.98.chr.gtf | grep protein_coding | cut -f1 | sort | uniq -c
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written by iraun iraun

thanks!!. It worked perfectly!

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written by Diego • Diego

Glad it helped :). Please consider marking the answer as "accepted" :).

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written by iraun iraun

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