adding gene and CDS feature types in ensemble gtf annotation with transcript and exon features

Question

[memy]

Hi

I am looking for adding gene and CDS feature into my ensembl GTF annotation file and appreciate your help.

chr01   ensembl transcript      16321180        16321695        .       -       .       gene_id "annotation_36"; transcript_id "annotation_45"; biotype "protein_coding"; translation_coords "16321671:16321695:1:16321180:16321403:224";
chr01   ensembl exon    16321671        16321695        .       -       .       gene_id "annotation_36"; transcript_id "annotation_45"; exon_number "1";
chr01   ensembl exon    16321583        16321634        .       -       .       gene_id "annotation_36"; transcript_id "annotation_45"; exon_number "2";
chr01   ensembl exon    16321440        16321531        .       -       .       gene_id "annotation_36"; transcript_id "annotation_45"; exon_number "3";
chr01   ensembl exon    16321180        16321403        .       -       .       gene_id "annotation_36"; transcript_id "annotation_45"; exon_number "4";
chr01   ensembl transcript      16321064        16322597        .       -       .       gene_id "annotation_36"; transcript_id "annotation_46"; biotype "protein_coding"; translation_coords "16321955:16322597:1:16321064:16321864:800";
chr01   ensembl exon    16321955        16322597        .       -       .       gene_id "annotation_36"; transcript_id "annotation_46"; exon_number "1";
chr01   ensembl exon    16321064        16321864        .       -       .       gene_id "annotation_36"; transcript_id "annotation_46"; exon_number "2";
chr01   ensembl transcript      16321064        16322597        .       -       .       gene_id "annotation_36"; transcript_id "annotation_47"; biotype "protein_coding"; translation_coords "16322232:16322597:1:16321064:16321684:621";
chr01   ensembl exon    16322232        16322597        .       -       .       gene_id "annotation_36"; transcript_id "annotation_47"; exon_number "1";
chr01   ensembl exon    16321955        16322197        .       -       .       gene_id "annotation_36"; transcript_id "annotation_47"; exon_number "2";
chr01   ensembl exon    16321718        16321864        .       -       .       gene_id "annotation_36"; transcript_id "annotation_47"; exon_number "3";
chr01   ensembl exon    16321064        16321684        .       -       .       gene_id "annotation_36"; transcript_id "annotation_47"; exon_number "4";

After adding gene feature

chr01   ensembl gene      16321180        16321684        .       -       .       gene_id "annotation_36";
chr01   ensembl transcript      16321180        16321695        .       -       .       gene_id "annotation_36"; transcript_id "annotation_45"; biotype "protein_coding"; translation_coords "16321671:16321695:1:16321180:16321403:224";
chr01   ensembl exon    16321671        16321695        .       -       .       gene_id "annotation_36"; transcript_id "annotation_45"; exon_number "1";
chr01   ensembl exon    16321583        16321634        .       -       .       gene_id "annotation_36"; transcript_id "annotation_45"; exon_number "2";
chr01   ensembl exon    16321440        16321531        .       -       .       gene_id "annotation_36"; transcript_id "annotation_45"; exon_number "3";
chr01   ensembl exon    16321180        16321403        .       -       .       gene_id "annotation_36"; transcript_id "annotation_45"; exon_number "4";
chr01   ensembl transcript      16321064        16322597        .       -       .       gene_id "annotation_36"; transcript_id "annotation_46"; biotype "protein_coding"; translation_coords "16321955:16322597:1:16321064:16321864:800";
chr01   ensembl exon    16321955        16322597        .       -       .       gene_id "annotation_36"; transcript_id "annotation_46"; exon_number "1";
chr01   ensembl exon    16321064        16321864        .       -       .       gene_id "annotation_36"; transcript_id "annotation_46"; exon_number "2";
chr01   ensembl transcript      16321064        16322597        .       -       .       gene_id "annotation_36"; transcript_id "annotation_47"; biotype "protein_coding"; translation_coords "16322232:16322597:1:16321064:16321684:621";
chr01   ensembl exon    16322232        16322597        .       -       .       gene_id "annotation_36"; transcript_id "annotation_47"; exon_number "1";
chr01   ensembl exon    16321955        16322197        .       -       .       gene_id "annotation_36"; transcript_id "annotation_47"; exon_number "2";
chr01   ensembl exon    16321718        16321864        .       -       .       gene_id "annotation_36"; transcript_id "annotation_47"; exon_number "3";
chr01   ensembl exon    16321064        16321684        .       -       .       gene_id "annotation_36"; transcript_id "annotation_47"; exon_number "4";

Answer 1

[Pratik]

As a note, you can do these kinds of operations in R as well using GenomicFeatures and it's associated packages. I'm not sure what your end objective is here.

Regardless, this should help you accomplish this in bash:

awk '$3 == "gene" || $3 == "transcript" || $3 == "CDS"' /home/pmehta/Downloads/Homo_sapiens.GRCh38.111.chr.gtf

replace /home/pmehta/Downloads/Homo_sapiens.GRCh38.111.chr.gtf with the location of your .gtf file.

---

This will extract all lines that have the following matches in column 3 ($3): gene, transcript, and CDS.

I think what you did was use grep with gene, but I think that matched gene_id in column 9.