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

[Colin <col...@gm...>]

The line that produces the "box" features with no exons is
P9424_ctg_01    AUGUSTUS    gene    220129  221909  .   -   .
ID=nbisL1-transcript-10667

This has no children and is just a box. If you load your data using --type
mRNA in flatfile-to-json it would filter out the gene level features. The
topLevelFeatures may help also

-Colin

On Sun, Mar 20, 2022 at 11:37 AM Nathan Dunn <nd...@gm...> wrote:

>
> Some quick thoughts:
>
> 1 - maybe get rid of the introns.   Not sure if Apollo filters them out or
> not.
>
> 2 - I think having 2 genes in the same track at the same location may be
> problematic, the latter one looks problematic.
>
> 3 - I *think* (if the problem. Persists) you can remove the “gene”
> annotation OR potentially (and better), you could add the
> “topLevelFeature”:”mRNA” as this example below.
>
> {"storeClass":"JBrowse/Store/SeqFeature/GFF3",
> "urlTemplate":"raw/824131860720236.gff", "label":"824131860720236",
> "type":"JBrowse/View/Track/HTMLFeatures", "style":{"className":"feature"},
> "key":"824131860720236", "topLevelFeatures":"mRNA",
> "apollo":{"source":"upload", "type":"GFF3", "topType":"mRNA"}}
>
> Those are my quick guesses.
>
> Nathan
>
> On Mar 18, 2022, at 6:50 PM, Johannes Debler <joh...@gm...>
> wrote:
>
> 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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