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2015-BMMB852D:AppliedBioinforma8cs
Week15,Lecture30
IstvánAlbert
BiochemistryandMolecularBiologyandBioinforma8csConsul8ngCenter
PennState
RNA-SeqconceptsAnRNA-Seqanalysishasthreeseparateyetequallyimportantsteps
1. Iden8fy/assignreadstoloca8ons
2. Es8ma8ngabundancespertranscript
3. Comparingabundancesàdifferen8alexpression
Thereisenormousdisagreementabouthoweachthesestepsshouldbeperformedàhenceverylargenumberofop8onsThereareworkflowsthatdoallthree.Thereareworkflowsthatmixandmatchfrommethods.
Makingsenseofyourdata
Soyou’veiden8fiedthetranscriptsthatdifferen8allyexpressacrosscondi8ons.
Nowwhat?
Thelengthyprocessofmakingsenseofdata
Themostimportantaspect
Don’texpectthedatatobothtellyouwhattheques:onis
andalsoprovidetheanswerforitHaveaques8on/hypothesisàthedatacananswerit.
Makingsensetakeslongerthanrunningtoolson
IPathwayguide–freetolookbutthencostsmoney
ErmineJ
Genesetanalysis
Paralysisofchoice
• Toomanychoices–toomanyparameters
• Whattopick,amIright
• I’veseenexcellentstudentsstrugglewiththis
Trustyourselfandmoveon.Finishingthejobishardest.
Bioinforma8cscanbestressful
Beingtheonlyonethatunderstandshowtoperformsomeanalyseshashighsandlows• Youcanbepartoflotsofpapers• EasiertomakeyourownsuccessLotsoftruthinMickWatson’samusingblogpos:• Aguidetothelonely(pet)bioinforma8cian
Genomics
Genomicsisthemostdifficult
ques8onhumanityhasevertakenon.
Beingpartofitisamazing.
Youarepartofthe0.0001%ofpopula8on
Enjoytheride!