"reference sequence not available" in "view details" when using indexed fasta #719

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billzt opened this Issue Mar 30, 2016 · 2 comments

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@billzt
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billzt commented Mar 30, 2016

My reference sequences are loaded by indexed fasta:

      {
         "urlTemplateFAI" : "seq/genome_Garb_JBrowse.fa.fai",
         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
         "urlTemplate" : "seq/genome_Garb_JBrowse.fa",
         "label" : "DNA",
         "type" : "SequenceTrack",
         "category" : "Reference sequence",
         "key" : "Reference sequence"
      },

My GFF file is loaded in a normal way:

      {
         "style" : {
            "className" : "feature"
         },
         "key" : "Protein Coding Gene",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : "CanvasFeatures",
         "urlTemplate" : "tracks/protein_coding_gene/{refseq}/trackData.jsonz",
         "compress" : 1,
         "category" : "Feature Annotation",
         "label" : "protein_coding_gene",
         "type" : "CanvasFeatures"
      },

In the "view detail" diaglog, it says:
Region sequence: reference sequence not available

b

Why?

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cmdcolin Mar 30, 2016

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I think you can add "useAsRefSeqStore": true to the config for the sequence track to fix this particular issue, but it might be a bug where the prepare-refseqs.pl for indexed fasta didn't output that properly. Will need to check and fix that if true

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cmdcolin commented Mar 30, 2016

I think you can add "useAsRefSeqStore": true to the config for the sequence track to fix this particular issue, but it might be a bug where the prepare-refseqs.pl for indexed fasta didn't output that properly. Will need to check and fix that if true

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billzt Apr 1, 2016

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Thank you. After add "useAsRefSeqStore": true, the bug is fixed.

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billzt commented Apr 1, 2016

Thank you. After add "useAsRefSeqStore": true, the bug is fixed.

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