remove 'transcript' track

[Johannes Debler]

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

[Nathan Dunn]

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

<image.png>

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[Johannes Debler]

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

[Nathan Dunn]

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

[Colin]

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

[Johannes Debler]

Thanks Colin,

reloading the file with --type mRNA did indeed filter out the box from being displayed.

Cheers.