Re: [Gmod-ajax] [apollo] remove 'transcript' track

[Johannes D. <joh...@gm...>]

Hi Nathan,

I think it is something odd that came out of combining braker 1 and 2
results. This is one particular gene annotation, have a look at the first
and last line, there are two 'gene' annotations for the same location with
different IDs.
Is there a way to display CDS features only?
Cheers,
Johannes

P9424_ctg_01    AUGUSTUS    gene    220129  221909  1   -   .
ID=nbis-gene-289;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    mRNA    220129  221909  1   -   .
ID=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;Parent=nbis-gene-289;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    exon    220129  221050  .   -   .
ID=exon-29374;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    exon    221100  221660  .   -   .
ID=exon-29375;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    exon    221746  221909  .   -   .
ID=exon-29376;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    CDS 220129  221050  1   -   1
ID=cds-29377;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    CDS 221100  221660  1   -   1
ID=cds-29378;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    CDS 221746  221909  1   -   0
ID=cds-29379;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    intron  221051  221099  1   -   .
ID=intron-18711;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    intron  221661  221745  1   -   .
ID=intron-18712;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    start_codon 221907  221909  .   -   0
ID=start_codon-10667;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    stop_codon  220129  220131  .   -   0
ID=stop_codon-10667;Parent=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1;gene_id=g_3228;transcript_id=anno2.P9424_ctg_01-_file_1_file_1_g9724.t1
P9424_ctg_01    AUGUSTUS    gene    220129  221909  .   -   .
ID=nbisL1-transcript-10667

On Fri, 18 Mar 2022 at 23:12, Nathan Dunn <nd...@gm...> wrote:

>
> Sometimes it does that if there is a top-level gene.
>
> Maybe a more of a JBrowse so cross-posting.
>
> Could you post the GFF3 snippet?
>
> Nathan
>
>
> On Mar 18, 2022, at 12:58 AM, Johannes Debler <joh...@gm...>
> wrote:
>
> Hi,
> I cannot figure out why for some uploaded GFF files Apollo displays the
> exon structure only, but for some it also displays a 'transcript' track
> (the blue and gray one underneath all the CDS features). I have removed
> 'transcript' from the GFF but it still displays it. Any idea how to make
> that go away?
> Cheers,
> Johannes
>
>
> <image.png>
>
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