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add more test data

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malachig committed Dec 4, 2015
1 parent 32c3a22 commit 536c4f1f43dbc9cfff99625c58794db7e3757767
Showing with 46 additions and 4 deletions.
  1. +7 −4 TODO.md
  2. +39 −0 tests/integration-test/data/hcc1395_igv_session.xml
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11 TODO.md
@@ -26,13 +26,16 @@ rm -fr SpliceJunctionSummary.R.stderr summary SpliceJunctionSummary.R.stdout Ens
###MGI datasets for testing regtools analysis
Requirements: WGS (or exome maybe) and RNA-seq on the same sample. Ideally a tumor/normal pair where we have RNA-seq for a matched adjacent normal.
#Look for a model/build to use
genome model rna-seq list --filter subject.name=H_NJ-HCC1395-HCC1395_RNA --show id,processing_profile,last_complete_build.id,last_complete_build.merged_alignment_result.bam_path --noheaders --style tsv | grep -v NULL
**HCC1395 (no matched adjacent normal, but there is a matched blood normal with RNA-seq)**
Tumor RNA-seq model: 5602f6df362745898b689c871714cfa2
Tumor WGS model: c6b40b160f60484bab5668dcdbbae681
Normal WGS model: 959e3cd8c5e14008b99f203d6c40b7c2
Normal WGS model: 2891325882
Tumor WGS model: 2891325873
Tumor RNA-seq model: 060145d385274d258569a9fc013e4ada
```
genome model list --filter 'id in [5602f6df362745898b689c871714cfa2,c6b40b160f60484bab5668dcdbbae681,959e3cd8c5e14008b99f203d6c40b7c2]' --show last_complete_build.merged_alignment_result.bam_path --noheaders | perl -ne 'print "https://gscweb.gsc.wustl.edu$_"'
genome model list --filter 'id in [2891325882,2891325873,060145d385274d258569a9fc013e4ada]' --show last_complete_build.merged_alignment_result.bam_path --noheaders | perl -ne 'print "https://gscweb.gsc.wustl.edu$_"'
```
- ALL1 (no matched adjacent normal, but we can use the 'healthy' normals for comparison)
@@ -0,0 +1,39 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<Session genome="b37" hasGeneTrack="true" hasSequenceTrack="true" locus="All" path="/Users/mgriffit/git/regtools/tests/hcc1395_igv_session.xml" version="8">
<Resources>
<Resource path="https://gscweb.gsc.wustl.edu/gscmnt/gc8002/info/build_merged_alignments/merged-alignment-blade9-3-2.gsc.wustl.edu-jwalker-2798-7169f237d9e043f7a08564a0c1c3cae4/7169f237d9e043f7a08564a0c1c3cae4.bam"/>
<Resource path="https://gscweb.gsc.wustl.edu/gscmnt/gc13001/info/build_merged_alignments/merged-alignment-blade11-2-10.gsc.wustl.edu-apipe-builder-32358-135679530/135679530.bam"/>
<Resource path="https://gscweb.gsc.wustl.edu/gscmnt/gc8002/info/build_merged_alignments/merged-alignment-blade14-4-3.gsc.wustl.edu-apipe-builder-18098-135585350/135585350.bam"/>
</Resources>
<Panel height="162" name="Panel1449187048115" width="1133">
<Track altColor="0,0,178" autoScale="true" color="175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="https://gscweb.gsc.wustl.edu/gscmnt/gc8002/info/build_merged_alignments/merged-alignment-blade14-4-3.gsc.wustl.edu-apipe-builder-18098-135585350/135585350.bam_coverage" name="Normal WGS" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
<DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="60.0" minimum="0.0" type="LINEAR"/>
</Track>
<Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="https://gscweb.gsc.wustl.edu/gscmnt/gc8002/info/build_merged_alignments/merged-alignment-blade14-4-3.gsc.wustl.edu-apipe-builder-18098-135585350/135585350.bam" name="135585350.bam" showSpliceJunctions="false" sortable="true" visible="true">
<RenderOptions colorByTag="" colorOption="FIRST_OF_PAIR_STRAND" flagUnmappedPairs="false" groupByTag="" maxInsertSize="1000" minInsertSize="50" shadeBasesOption="QUALITY" shadeCenters="true" showAllBases="false" sortByTag=""/>
</Track>
</Panel>
<Panel height="168" name="Panel1449187060070" width="1133">
<Track altColor="0,0,178" autoScale="true" color="175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="https://gscweb.gsc.wustl.edu/gscmnt/gc13001/info/build_merged_alignments/merged-alignment-blade11-2-10.gsc.wustl.edu-apipe-builder-32358-135679530/135679530.bam_coverage" name="Tumor WGS" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
<DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="60.0" minimum="0.0" type="LINEAR"/>
</Track>
<Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="https://gscweb.gsc.wustl.edu/gscmnt/gc13001/info/build_merged_alignments/merged-alignment-blade11-2-10.gsc.wustl.edu-apipe-builder-32358-135679530/135679530.bam" name="135679530.bam" showSpliceJunctions="false" sortable="true" visible="true">
<RenderOptions colorByTag="" colorOption="FIRST_OF_PAIR_STRAND" flagUnmappedPairs="false" groupByTag="" maxInsertSize="1000" minInsertSize="50" shadeBasesOption="QUALITY" shadeCenters="true" showAllBases="false" sortByTag=""/>
</Track>
</Panel>
<Panel height="168" name="Panel1449187069629" width="1133">
<Track altColor="0,0,178" autoScale="true" color="175,175,175" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="https://gscweb.gsc.wustl.edu/gscmnt/gc8002/info/build_merged_alignments/merged-alignment-blade9-3-2.gsc.wustl.edu-jwalker-2798-7169f237d9e043f7a08564a0c1c3cae4/7169f237d9e043f7a08564a0c1c3cae4.bam_coverage" name="Tumor RNA-seq" showReference="false" snpThreshold="0.2" sortable="true" visible="true">
<DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="60.0" minimum="0.0" type="LINEAR"/>
</Track>
<Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="EXPANDED" featureVisibilityWindow="-1" fontSize="10" id="https://gscweb.gsc.wustl.edu/gscmnt/gc8002/info/build_merged_alignments/merged-alignment-blade9-3-2.gsc.wustl.edu-jwalker-2798-7169f237d9e043f7a08564a0c1c3cae4/7169f237d9e043f7a08564a0c1c3cae4.bam" name="7169f237d9e043f7a08564a0c1c3cae4.bam" showSpliceJunctions="false" sortable="true" visible="true">
<RenderOptions colorByTag="" colorOption="FIRST_OF_PAIR_STRAND" flagUnmappedPairs="false" groupByTag="" maxInsertSize="1000" minInsertSize="50" shadeBasesOption="QUALITY" shadeCenters="true" showAllBases="false" sortByTag=""/>
</Track>
</Panel>
<Panel height="64" name="FeaturePanel" width="1133">
<Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="Reference sequence" name="Reference sequence" sortable="false" visible="true"/>
<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" colorScale="ContinuousColorScale;0.0;251.0;255,255,255;0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" height="35" id="b37_genes" name="Gene" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count">
<DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="251.0" minimum="0.0" type="LINEAR"/>
</Track>
</Panel>
<PanelLayout dividerFractions="0.01020408163265306,0.2942176870748299,0.5884353741496599,0.8826530612244898"/>
</Session>

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