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Gff3tabix representation not informative or absent #1103

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thomasvangurp opened this Issue Jul 10, 2018 · 4 comments

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thomasvangurp commented Jul 10, 2018

I have loaded several tracks using a tabix-indexed bgzipped GFF3 file in a genome browser (not publicly accesible :-( ). The feature density display is not workable for me currently. When I compare a feature density display for the same track data comparing "storeClass": "JBrowse/Store/SeqFeature/NCList", and "storeClass": "JBrowse/Store/SeqFeature/GFF3Tabix", the display for the NClist is working: see solgenomics jbrowse
jbrowse_st4_03ch02_1__47313589

wheras the gff3tabix track displays the following:
solynta_jbrowse_chr02_383167__48295469

Zoomed in both tracks work as they should. For the gene tracks I do get a display of some features, but is is very sparse:
solynta_jbrowse_chr02_6533569__38291147

Could is be that the interval size of the tbi files is simply to big to be usefull for displaying a rich and detailed feature density plot? If that's the case, would csi indexes solve this issue? see my comment in #1086

@rbuels rbuels added the user support label Jul 10, 2018

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cmdcolin commented Jul 10, 2018

@thomasvangurp do you have any additional information about this? I am not sure I am able to reproduce this issue. Did you make a new track using GFF3Tabix in the second picture that was based on the NCList data in the first picture?

Also what JBrowse version are you using? Note that JBrowse 1.14.1 added better histograms for GFF3Tabix (see release-notes and #1039)

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cmdcolin commented Jul 13, 2018

@thomasvangurp any update on this? is there a sample data file that helps recreate this issue?

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thomasvangurp commented Jul 16, 2018

@cmdcolin Sorry for the delay, i made the new config using gff3tabix, this is entry (without the "style" and "menutemplate" option:

{         
"key" : "PGSC DM v4.03 gene models",
         "trackType" : "CanvasFeatures",
         "storeClass" : "JBrowse/Store/SeqFeature/GFF3Tabix",
         "maxFeatureScreenDensity" : 0.05,
         "urlTemplate" : "solgenomics_tracks/gene_models/PGSC_DM_V403_genes.gff3.gz",
         "tbiurlTemplate" : "solgenomics_tracks/gene_models/PGSC_DM_V403_genes.gff3.gz.tbi",
         "storeTimeout" : 10000,
         "metadata" : {
            "category" : "solgenomics/Gene models",
            "description" : "Gene models from PGSC for S. tuberosum Group Phureja DM1-3 Genome Annotation v3.4 mapped to v4.03"
         },
         "type" : "CanvasFeatures",
         "label" : "gene_models"
      },

I am running Jbrowse 1.14.2. You can download the potato genome here: http://solanaceae.plantbiology.msu.edu/data/potato_dm_v404_all_pm_un.fasta.zip

The tabix indexed gff3.gz are attached (note that the .tbi file has the .txt extension attached as uploading a .tbi file is not permitted by github):

PGSC_DM_V403_genes.gff3.gz

PGSC_DM_V403_genes.gff3.gz.tbi.txt

please let me know if you can reproduce the issue with the data attached.

EDIT:
this is the track config as used by jbrowse:

{
  "maxFeatureSizeForUnderlyingRefSeq": 250000,
  "subfeatureDetailLevel": 2,
  "maxFeatureScreenDensity": 0.05,
  "enableCollapsedMouseover": false,
  "disableCollapsedClick": false,
  "maxFeatureGlyphExpansion": 500,
  "maxHeight": 600,
  "histograms": {
    "description": "feature density",
    "min": 0,
    "height": 100,
    "color": "goldenrod",
    "clip_marker_color": "red"
  },
  "style": {
    "_defaultHistScale": 4,
    "_defaultLabelScale": 30,
    "_defaultDescriptionScale": 120,
    "showLabels": true,
    "showTooltips": true,
    "label": "id",
    "description": "name",
    "className": "feature",
    "linkTemplate": "http://solgenomics.net/search/quick?term={id}"
  },
  "displayMode": "normal",
  "events": {},
  "menuTemplate": [
    {
      "label": "View details",
      "title": "{type} {name}",
      "action": "contentDialog",
      "iconClass": "dijitIconTask"
    },
    {
      "label": "Highlight this gene",
      "iconClass": "dijitIconConnector"
    },
    {
      "label": "Ask SGN about {id}",
      "action": "newWindow",
      "iconClass": "dijitIconDatabase",
      "url": "http://solgenomics.net/search/quick?term={id}"
    },
    {
      "iconClass": "dijitIconDatabase",
      "action": "newWindow",
      "url": "http://www.ebi.ac.uk/ebisearch/search.ebi?db=proteinSequences&t={id}",
      "label": "Ask EMBL about {id}"
    },
    {
      "iconClass": "dijitIconDatabase",
      "action": "newWindow",
      "url": "http://www.google.com/search?q={id}",
      "label": "Ask Google about {id}"
    }
  ],
  "key": "PGSC DM v4.03 gene models",
  "trackType": "CanvasFeatures",
  "storeClass": "JBrowse/Store/SeqFeature/GFF3Tabix",
  "urlTemplate": "solgenomics_tracks/gene_models/PGSC_DM_V403_genes.gff3.gz",
  "tbiurlTemplate": "solgenomics_tracks/gene_models/PGSC_DM_V403_genes.gff3.gz.tbi",
  "storeTimeout": 10000,
  "metadata": {
    "category": "solgenomics/Gene models",
    "description": "Gene models from PGSC for S. tuberosum Group Phureja DM1-3 Genome Annotation v3.4 mapped to v4.03"
  },
  "type": "JBrowse/View/Track/CanvasFeatures",
  "label": "gene_models",
  "baseUrl": "http://my.url/data/Solanum_tuberosum_v4.04/existing_tracks/",
  "index": 2
}
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cmdcolin commented Jul 16, 2018

Should be fixed by #1123 ! Thanks so much for the good sample data and patience!!!

@cmdcolin cmdcolin closed this Jul 16, 2018

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