General anesthesia selectively disrupts astrocyte calcium signaling
Astrocyte –BioHPC Workflow Platform...Astrocyte –BioHPC Workflow Platform Standardized Workflows...
Transcript of Astrocyte –BioHPC Workflow Platform...Astrocyte –BioHPC Workflow Platform Standardized Workflows...
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
Browseworkflows
RNASeq Analysis Pipeline
http://www.utsouthwestern.edu/labs/bioinformatics/services/data-analysis/rnaseq-pipeline.html
RNAseq AnalysisEssence
• Preprocessingandnormalization• Differentialgeneexpressionanalysis• QC• Visualization• Pathwayandgenesetsenrichmentanalysis• Differentsplicingisoforms• Fusionandvariants
Createanewproject
Adddatatoyourproject
Adddatatoyourproject
ForNGSexperiment,thisisrecommended.
Makeyourdesignfile
Makeyourdesignfile• Usetabasdelimiter– Excelsaveas“Text(tabdelimited)”
• IfnoSubjectID,usesamenumber/characterforallrows
• SampleID andSampleName• IfnoFqR2,leavethemempty• Forallcontents,no“-”• Forallcontents,nospaces• ColumnsnamesMUSTbeexactlythesameasdocumented
Selectyourdatafilesandsetupworkflowandsubmit
SELECTYOURFILES
http://software.broadinstitute.org/gsea/msigdb/index.jsp
Projectisrunning
Timelineofthewholerun
Download/visualizeyourresults
Vizapp needabout30stostartifthereisnoqueue.Youneedtorefreshthepage.
Youcanalsochooseindividualfilestodownloadtoyourlocalcomputer
Comparisons• ComparisonsarebasedonSampleGroup– Allpair-wisecomparisons– Couldbeidentifiedbyfilename• A_B.edgeR.txt• LogfoldchangewillbeA/B• IfyouwantB/A,-1*logFC
Vizapp:QCgeneralstat
Vizapp:QCMSDandPCA
Vizapp:GeneCompare
Vizapp:DEA
• UsesedgeR results• Filtergenelistbydifferentparameters• Sortbydifferentcolumns• Datatabledownloading
Vizapp:DEAheatmap
• Filtergenelistbydifferentparameters• Choosedifferentcomparisons• Supportuserdefinegenelist(geneofficialsymbol)• Supportpathway
Vizapp:alternativesplicing
Differenttranscripts’expressioninsamplegroups
Vizapp:alternativesplicing
Vizapp:QuSAGE
Commonerrorsandsolutions
• Makesurethedelimiteristab• Makesurethecolumnnamearethesameasmentionedindocumentation
• Makesurethefilenamesmatch
Commonerrorsandsolutions
• Notallfilesareuploaded
• It’sabouttheproxysetting
• Useauto-detectproxy
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)