BAM file track

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Michał T. Lorenc

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Aug 19, 2022, 12:50:43 AM8/19/22
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Hi all,
The first BAM track comes from Star Aligner.

image.png

        {
            "storeClass": "JBrowse/Store/SeqFeature/BAM",
            "urlTemplate": "raw/Flower_BAM.bam",
            "style": {"className": "feature"},
            "label": "Flower_BAM",
            "apollo": {
                "source": "upload",
                "type": "BAM"
            },
            "type": "JBrowse/View/Track/Alignments",
            "category": "v. RNA-seq aligned reads",
            "key": "Flower_BAM"
        },


This one comes from Hi-sat2 aligner.

image.png


      {
         "key" : "NbRNASeq_Meristem_Feb2019",
         "label" : "NbRNASeq_Meristem_Feb2019",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "type" : "JBrowse/View/Track/Alignments",
         "urlTemplate" : "NbRNASeq_MstS.sorted.bam",
         "category" : "vi. Tracks Dev"
      },

How do I get the Star Aligner to look like a Hi-sat2 track?

Thank you in advance,

Best wishes,

Michal

Nathan Dunn

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Aug 19, 2022, 12:52:18 PM8/19/22
to "Michał T. Lorenc", apollo, gmod-ajax

Maybe set the type to Alignments2?  (Canvas). 



Nathan


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