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)