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Won't load track details from previous session xml file #1601
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I can't really debug this visually, and could not load it even if you uploaded as it references local files. If you can diff the BTW you can zip the XML file, or any other type, and upload the zipped file |
Here's a link to an example bam. Also attached a zipped xml. I didn't hand-edit it at all. igv_only_coverage.xml.zip Appreciate your help! |
I can't load your example BAM, it has non-standard sequence names (mm39_1, etc). |
I have an issue loading a previous session from a session xml file.
In a previous session, I changed the track height and set track colors to correspond to their conditions. However, when I reload the session from file, it loads in the tracks in the grey color and default height.
In the xml file, it specifies their custom height and color changes. I'm a little bit at a loss for why IGV doesn't incorporate these details.
I'm on macOS Sonoma 14.5. Plotting RNA-seq data. Below is my session session file in full text, since GitHub won't allow an XML file upload.
Thanks!
<?xml version="1.0" encoding="UTF-8" standalone="no"?> <Session genome="mm39" hasGeneTrack="true" hasSequenceTrack="true" locus="chr19:5034541-5037701" nextAutoscaleGroup="5" path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/igv_only_coverage.xml" version="8"> <Resources> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/dSE3.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d30m1.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d30m2.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d6h2.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/KA2.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d6h1.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/KA1.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/dSE2.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/dSE1.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/KA3.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d30m3.bam"/> <Resource path="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d6h3.bam"/> </Resources> <Panel height="900" name="DataPanel" width="2543"> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="30,136,229" colorScale="ContinuousColorScale;0.0;19.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/dSE1.bam_coverage" name="dSE1.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="19.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="30,136,229" colorScale="ContinuousColorScale;0.0;15.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/dSE2.bam_coverage" name="dSE2.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="15.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="30,136,229" colorScale="ContinuousColorScale;0.0;30.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/dSE3.bam_coverage" name="dSE3.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="30.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="216,27,96" colorScale="ContinuousColorScale;0.0;24.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d30m1.bam_coverage" name="d30m1.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="24.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="216,27,96" colorScale="ContinuousColorScale;0.0;57.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d30m2.bam_coverage" name="d30m2.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="57.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="216,27,96" colorScale="ContinuousColorScale;0.0;32.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d30m3.bam_coverage" name="d30m3.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="32.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="255,193,7" colorScale="ContinuousColorScale;0.0;19.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d6h1.bam_coverage" name="d6h1.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="19.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="255,193,7" colorScale="ContinuousColorScale;0.0;23.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d6h2.bam_coverage" name="d6h2.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="23.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="255,193,7" colorScale="ContinuousColorScale;0.0;29.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/d6h3.bam_coverage" name="d6h3.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="29.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="9,129,84" colorScale="ContinuousColorScale;0.0;807.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/KA1.bam_coverage" name="KA1.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="807.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="9,129,84" colorScale="ContinuousColorScale;0.0;1295.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/KA2.bam_coverage" name="KA2.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="1295.0" minimum="0.0" type="LINEAR"/> </Track> <Track autoScale="true" clazz="org.broad.igv.sam.CoverageTrack" color="9,129,84" colorScale="ContinuousColorScale;0.0;2392.0;255,255,255;175,175,175" fontSize="15" height="75" id="/Volumes/jack/seq/analysis_May2024/sublibrary1/process/sample_bams/KA3.bam_coverage" name="KA3.bam Coverage" snpThreshold="0.2" visible="true"> <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="2392.0" minimum="0.0" type="LINEAR"/> </Track> </Panel> <Panel height="285" name="FeaturePanel" width="2543"> <Track clazz="org.broad.igv.track.SequenceTrack" fontSize="10" height="72" id="Reference sequence" name="Reference sequence" visible="true"/> <Track altColor="0,0,178" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" colorScale="ContinuousColorScale;0.0;474.0;255,255,255;0,0,178" displayMode="EXPANDED" fontSize="10" height="73" id="mm39_genes" name="Gene" visible="true"/> </Panel> <PanelLayout dividerFractions="0.7544453852667231"/> <HiddenAttributes> <Attribute name="DATA FILE"/> <Attribute name="DATA TYPE"/> <Attribute name="NAME"/> </HiddenAttributes> </Session>
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