astrocyte –biohpc workflow platform...astrocyte –biohpc workflow platform standardized workflows...
TRANSCRIPT
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)