How to display Note's full description of "Feature" attribute in gtf/gff

[sadikmz]

Hi,

I could not able to display the functional annotation genes described under "Note" in gtf feature section but those in the gtf get truncated and only display the first word of the description for each gene (blue description in the figure).

Here's gff description for gene in left corner of the screenshot

chr07   Gmove   gene    33870033        33873924        2097    +       .       ID=Macma4_07_g22990;Name=Macma4_07_g22990
chr07   Gmove   mRNA    33870033        33873924        2097    +       .       ID=Macma4_07_g22990.1;Parent=Macma4_07_g22990;Name=Macma4_07_g22990.1;Note=putative Disease resistance RPP8-like protein 3
chr07   Gmove   exon    33870033        33870488        .       +       .       Parent=Macma4_07_g22990.1
chr07   Gmove   exon    33871719        33873924        .       +       .       Parent=Macma4_07_g22990.1
chr07   Gmove   CDS     33871828        33873924        .       +       0       Parent=Macma4_07_g22990.1
chr07   Gmove   UTR     33870033        33870488        .       +       .       Parent=Macma4_07_g22990.1
chr07   Gmove   UTR     33871719        33871827        .       +       .       Parent=Macma4_07_g22990.1

and the gtf for same gene

chr07   Gmove   gene    33870033        33873924        2097    +       .       gene_id "Macma4_07_g22990"; ID "Macma4_07_g22990"; Name "Macma4_07_g22990";
chr07   Gmove   mRNA    33870033        33873924        2097    +       .       gene_id "Macma4_07_g22990"; transcript_id "Macma4_07_g22990.1"; ID "Macma4_07_g22990.1"; Name "Macma4_07_g22990.1"; Note "putative Disease resistance RPP8-like protein 3"; Parent "Macma4_07_g22990";
chr07   Gmove   exon    33870033        33870488        .       +       .       gene_id "Macma4_07_g22990"; transcript_id "Macma4_07_g22990.1"; ID "agat-exon-120097"; Parent "Macma4_07_g22990.1";
chr07   Gmove   exon    33871719        33873924        .       +       .       gene_id "Macma4_07_g22990"; transcript_id "Macma4_07_g22990.1"; ID "agat-exon-120098"; Parent "Macma4_07_g22990.1";
chr07   Gmove   CDS     33871828        33873924        .       +       0       gene_id "Macma4_07_g22990"; transcript_id "Macma4_07_g22990.1"; ID "agat-cds-115016"; Parent "Macma4_07_g22990.1";
chr07   Gmove   UTR     33870033        33870488        .       +       .       gene_id "Macma4_07_g22990"; transcript_id "Macma4_07_g22990.1"; ID "agat-utr-34280"; Parent "Macma4_07_g22990.1";
chr07   Gmove   UTR     33871719        33871827        .       +       .       gene_id "Macma4_07_g22990"; transcript_id "Macma4_07_g22990.1"; ID "agat-utr-34281"; Parent "Macma4_07_g22990.1";

My aim is to display putative Disease resistance RPP8-like protein 3 and the same description under Name. But it is picking up the first word 'putative' when using the gtf (middle bars) and not displaying at all when using the gff (the bottom bars).

Any suggestions?

[cmdcolin]

I will have to check why the GTF isn't parsing correctly

for the GFF, if you move the "Note" up to the "gene" line, it will display (alternatively, you can remove the gene level but you may have to also refer references to the gene level line by removing the Parent= tag references)

[sadikmz]

Thanks for the suggestion. The suggestion on adding the "Note" in "gene" line worked for GFF.

Thanks a lot.