SPARoutputsandreportpage

Landingresultspage(fullview)

Landingresults/outputspage(top)

Jobidisshown

Inputfilesarelisted

Bookmark/ShareSPARresultslink

Downloadalltables,figures,tracksaszip

Percentageofreadsper

sncRNA class

TotalnumberofreadsAllprofiledsncRNA classes

Percentageofpeaksper

sncRNA class

Totalnumberofpeaks

Landingresults/outputspage(top)

Toviewareport(inhtml/pdf):Click“Linkto

results: https://www.lisanwanglab.org/SPAR/SPAR_out/ca8ac37

Landingresultsà SPARreportpage

Reportisavailableinhtml/pdf

SPARreport.pdfA15pagereportcontainingtablesandfiguresfordownloadandsharing

Landingresults/ outputspage(bottom)Summary

informationonreads

Afterclickingshowmoreatthebottomofthe“RunSummary”

Summaryinformationon

peaks Step1:Expandthistoviewtheinteractive

peakbrowser

InteractivePeakBrowser(Output)

Clickthistogoto“InteractivePeakBrowser”

InteractivePeakBrowser(Output)Totalnumberofcalledpeaks(annotatedorunannotated)

Click“pointingdownerror”toselectotherfeaturestodisplay

InteractivePeakBrowser(Output)

Step1:Type“95.”inthistextboxandclickenter

FiltersncRNA lociwiththetop5%ofexpression

Numberoflocithatpassedthiscriteria:60

InteractivePeakBrowser(Output)FurtherfiltersncRNA locithatonlypresentinPromoter,3’or5’UTRexonic regions

Step2:Select“Promoter”,“3’UTRExon”,“5”UTRExon”

Numberoflocithatfulfilledthesecriteria:4

Step3:Exportthese4filteredsncRNAs

Optional:clickthislinktovisualizethispeakP993inUCSCgenomebrowser

InteractivePeakBrowser(Output)Hg38reference

genome

Peakcoordinatesandlength

SPARPeakprofileonpositivestrandTissue:frontal

cortexPeakexpression

value

Annotation:mir484

ConfigurationforSPARtracks

FinishexploringInteractivePeakBrowser,nextviewpeaksingenomebrowser

Step1:clickthistominimizethis

section

Step2:clickthistomaximizethis

section

ViewinGenomeBrowser(Output)Optional:“ViewSPARresulttracksinUCSCGenomeBrowser(opensinthe

newwindow)”ifpreferred

DASHRannotationtracks

Typeingenomiccoordinates/RNA/genesymbolsofinterest

Zoominorout

SPARPeaks– positiveandnegative

SPARrawsignals– positiveandnegative

Expressionvalues

FinishexploringGenomebrowser,quicklyunderstandthedatainagenomewide view

Step1:clickthistominimizethis

section

Step2:clickthistomaximizethis

section

Plots(Output)– tonavigateacrossallplots4differentplotsessions

Step1:Clicktodisplay,correspondingplotwillbeshownintheright

Step2:Clickanywhereonthefiguretodisplaythefigureinanewtab

(fullpageview)

Plots(Output)– 14differentplotsessions

Clicktodisplay,correspondingplotwillbeshownintheright

Thisshowsaftersegmentation,ofallthelocithatareofacertainlength,the%of

sumofRPMvaluesoftheselocioverallloci

Plots(Output)- 2

Thisshowsaftersegmentation,thelengthdistributionofallcalledloci

Thisshowsmostofthepeaksarebetween15-17nt long

Plots(Output)- 3

ThisshowsthedistributionofRPMvaluesforlociper

RNAclasses

ThepercentileofRPM(50%,75%and90%)valuesareshownhere

ThisshowstRF3arelowlyexpressed,comparedto

otherclasses

Plots(Output)– 4

Alllociaregroupedbyclasses,countsshowninbrackets.

Forlociineachclass,wedividedthemintogroupsofspecificlength(xaxis).Eachsmall“block”inthisheatmap

showsthenormalizedRPMvaluesoflociofspecificlengthforeachRNAclass.

A“Block”

Thisshowsthereare192mir-3ploci,the22ntonesarethemosthighlyexpressed.

Plots(Output)- 5

sncRNA geneannotationsstartat“0.0”

SmallRNAclass

WithrespecttothesncRNA geneannotation,thegenomewidelocationofwherethesncRNA lociarecalled.E.g.90sncRNAs oftRF-5-trfdbstartsatthe1st positionoftheannotation,meaningthe“processingpatterns”oftheselociarevery

specificforthisclass

ThisshowsthesnoRNA locicalledarelyingindifferentpartsofthesnoRNA

gene,inferringtheymayhavedifferentprocessingmechanisms

Plots(Output)- 6

Theplotshowsthedistributionof%ofreadsthatarewiththesame5’end.Thehigherthevalues,

meaningthatmostreadshavethesame5’end,e.g.mir-5p,tRF-1-trfdb,unannot inthisfigure

Plots(Output)- 7

Thisshowsthedistributionofthescore“processingspecificityatthe5’end”acrosslociforeach

sncRNA classes

Thecloserthevaluesto1,themorespecifictheprocessing

patternsare,e.g.mir-3p,mir-5p,mir-5p3pno,tRF-1-trfdb,unanno

Plots(Output)- 8

TheplotcomparespersncRNA class,thecountofRNAlocicharacterized/discoveredtothatofthefullannotations.Thehigherthepercentage,meaningthatthemorecanonical

lociarepresentinthedata.

Plots(Output)- 9

ThisplotshowspersncRNA class,whichgenomicelementstheyresidein.Takemir-3pasanexample,mostmir-3presidesinintergenicregion,followedbymRNAintrons,3’UTRintronsand5’intronsregions(i.e.

intronic regions).AtinyamountfallsintomRNAexonregions.

Plots(Output)- 10

Thisplotshowsthegenomewideexpressionvalues(RPM)acrossallthechromosomes.E.g.therearenocharacterizedtRNAs from

chr3andchr4forthisdata

Plots(Output)- 11

ThisplotshowsthepercentageofmappedreadsperlociperRNAclass.E.g.mosttothereadsfallintomiRNAclasses,followedbyunannotatedloci

Finishviewingtheplots,wanttoperformownanalyseswithSPARresults– visitdownload

Step1:clickthistominimizethis

section

Step2:clickthistomaximizethis

section

Downloadresults(Top)– sncRNA geneexpression

Step1:ClicktodownloadsncRNA geneexpressiondata(insteadofindividualloci’

RPMwillbeshown)

Tracksforbrowsing

Downloadresults(Output)- sncRNA geneexpression

Under“GeneExpression”section“smRNA_gene_expression.xls”:

Thistabledisplaysthereadcounts,aswellasRPMexpressionvaluesforthesncRNAgenesidentified sncRNA gene

name

Downloadresults(Top)– comparisonexpressionresultswithDASHR/ENCODE(1)

Step2:Clicktodownloadpeakspresentinboththeanalysed dataandalsoexpressedinDASHR

Comparisonexpressiontables

Downloadresults– comparisonexpressiontables(usingDASHRasexample)

Under“ComparisonwithDASHR”,download“DASHR_comparison_all.xls”Calledpeak

annotationandfeatures

ComparisoncolumnswithallDASHRtissues(atotalof54columns) ……

Downloadresults(Top)– comparisonexpressionresultswithDASHR/ENCODE(2)

Comparisonexpressiontables

Step3:Clicktodownloadpeaksonlyinanalysed data

butnotinDASHR

Downloadresults– comparisonexpressiontables(usingDASHRasexample)

Under“ComparisonwithDASHR”,download“not_in_DASHR.xls”Calledpeak

annotationandfeatures

ComparisoncolumnswithallDASHRtissues(atotalof54columns) ……

Sincethislociarecharacterizedintheanalyzeddata,butnotinDASHR,thereforethesecolumnsdonotcontainand

informationfromDASHR

Downloadresults(Bottom)–downloadbysncRNA class

Step1:Clicktodownload,e.g.tRNA onlylociresultsfromSPAR

TotalnumberofreadsfallingontothisRNAclass

Downloadresults(Output)“peaks.byClass.tRNA.xls”showsallthetRNAs onlylociresultsfromSPAR tRNA

Downloadresults(Bottom)–downloadbysncRNA class

Step2:Clicktodownload,e.g.allunannotatedlocifromSPAR

TotalnumberofreadsfallingontothisRNAclass

Optional:ClicktodownloadallannotatedlocifromSPAR

Downloadresults(Output)“peaks_unannot.xls”under“PeakTables”showalltheunannotatedpeaksfoundbyrunningSPAR No

annotation

Runlog(Output)Step1:clickthistominimize

“Downloadresults”

Step2:clickthistomaximize“Runlog”

Runlog(Output) Runlogdisplayedagin

Sendquestionstothisemail:SPAR@lisanwanglab.org

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