Astrocyte –BioHPC Workflow Platform...Astrocyte –BioHPC Workflow Platform Standardized Workflows...
Transcript of Astrocyte –BioHPC Workflow Platform...Astrocyte –BioHPC Workflow Platform Standardized Workflows...
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Allows groups to give easy-access to their analysis pipelines via the web
Astrocyte – BioHPC Workflow Platform
StandardizedWorkflows
SimpleWebForms
Onlinedocumentation&resultsvisualization*
WorkflowsrunonHPCclusterwithoutdeveloperoruserneedingclusterknowledge
Slidecontribution:DavidTrudgian@BioHPC
astrocyte.biohpc.swmed.edu
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Browseworkflows
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RNASeq Analysis Pipeline
http://www.utsouthwestern.edu/labs/bioinformatics/services/data-analysis/rnaseq-pipeline.html
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RNAseq AnalysisEssence
• Preprocessingandnormalization• Differentialgeneexpressionanalysis• QC• Visualization• Pathwayandgenesetsenrichmentanalysis• Differentsplicingisoforms• Fusionandvariants
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Createanewproject
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Adddatatoyourproject
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Adddatatoyourproject
ForNGSexperiment,thisisrecommended.
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Makeyourdesignfile
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Makeyourdesignfile• Usetabasdelimiter– Excelsaveas“Text(tabdelimited)”
• IfnoSubjectID,usesamenumber/characterforallrows
• SampleID andSampleName• IfnoFqR2,leavethemempty• Forallcontents,no“-”• Forallcontents,nospaces• ColumnsnamesMUSTbeexactlythesameasdocumented
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Selectyourdatafilesandsetupworkflowandsubmit
SELECTYOURFILES
http://software.broadinstitute.org/gsea/msigdb/index.jsp
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Projectisrunning
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Timelineofthewholerun
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Download/visualizeyourresults
Vizapp needabout30stostartifthereisnoqueue.Youneedtorefreshthepage.
Youcanalsochooseindividualfilestodownloadtoyourlocalcomputer
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Comparisons• ComparisonsarebasedonSampleGroup– Allpair-wisecomparisons– Couldbeidentifiedbyfilename• A_B.edgeR.txt• LogfoldchangewillbeA/B• IfyouwantB/A,-1*logFC
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Vizapp:QCgeneralstat
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Vizapp:QCMSDandPCA
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Vizapp:GeneCompare
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Vizapp:DEA
• UsesedgeR results• Filtergenelistbydifferentparameters• Sortbydifferentcolumns• Datatabledownloading
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Vizapp:DEAheatmap
• Filtergenelistbydifferentparameters• Choosedifferentcomparisons• Supportuserdefinegenelist(geneofficialsymbol)• Supportpathway
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Vizapp:alternativesplicing
Differenttranscripts’expressioninsamplegroups
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Vizapp:alternativesplicing
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Vizapp:QuSAGE
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Commonerrorsandsolutions
• Makesurethedelimiteristab• Makesurethecolumnnamearethesameasmentionedindocumentation
• Makesurethefilenamesmatch
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Commonerrorsandsolutions
• Notallfilesareuploaded
• It’sabouttheproxysetting
• Useauto-detectproxy
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Additionalwebsiteformoreoptionsondatareport
• GeneSetEnrichmentAnalysis(GSEA)http://software.broadinstitute.org/gsea/index.jspMSigDBhttp://software.broadinstitute.org/gsea/msigdb/index.jspGenePatternhttp://software.broadinstitute.org/cancer/software/genepattern/
• Userdesignedspecificheatmaps byMorpheushttps://software.broadinstitute.org/morpheus/
• ComplexdesignsFactorialdesignsinedgeR orDEseq fromcountTable.csv
• Motifsearch/promoteranalysiswithHomermotifsearchDifferentregulatedgenelist(edgeR.result)