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single cell rna sequencing data analysis, 25-29 january 2021...course_intro_asa_bjorklund_2021...

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Single cell RNA sequencing data analysis, 25-29 January 2021 Åsa Björklund & Paulo Czarnewski [email protected]

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  • SinglecellRNAsequencingdataanalysis,25-29January2021

    ÅsaBjörklund&[email protected]

  • Whoarewe?

    Main:

    ÅsaBjörklundPauloCzarnewskiNBIS/UUNBIS/SU

    TAs:

    Lectureres:

    KarolinaWallenborg AlmaAndersson NikolayOskolkov AhmedMahfouzESCG/Scilifelab KTH/Spatial NBIS/LULeidenU

    ErikFasterius JonathanRobinson AnnaJohannson Lokesh ManoharanNBIS/SUNBIS/ChalmersNBIS/UUNBIS/LU

  • NationalBioinformaticsInfrastructureSweden(NBIS)

    3

    Futurecomputeinfrastructure

    Consultations

    Training

    Researchsupport

    Efficienttoolsandworkflows

    DatapublishingandopenscienceSecuresharingofsensitivedata

    ComputeprojectsSoftwareanddatabases

  • NeedhelpfromNBIS?

    • Drop-insessionsatalluniversities(nowonline)14.00Tuesdays

    • Consultations• Courses• Support:• Long-termsupport(Peerreviewed)• Fee-for-servicesupport,hourlyfee• Partnerprojects

    • Datacenter

    www.nbis.se

  • Practicalinformation

    • Alllectures/exerciseswillbeheldonthiszoomlink.• Weaskallparticipantstokeeptherecameraon,butpleasemuteunlessyouhavesomequestions.

    • Ifyouhavequestions:– Justunmuteandaskdirectly.– Raiseyourhandinzoom– Askthequestioninthezoomchat/slackchannel#questions

    • Wehaveincludedmanybreaks– takethechancetostretchyourlegstoavoidzoomfatigue!

  • Practicalinformation- Slack

    • Communicationaroundthecoursewillbehandledviaslack.

    • Pleaseaddpictureandbriefdescription• Channels:– #general– generalinformationaboutthecourse– #exercises– questionsduringexercises– #installation_issues – questionsabouttheinstallations– #group1,2,3,4,5,aforeachgrouptocommunicate– #questions– postanyquestionregardingthecoursecontent.

  • scRNA-seq overview

    • Whatmethod….

    Rawdata:fastq files

    • Smartseq2/3• 10x• CITE-seq• SPLIT-seq• ….

    Dataanalysis

  • scRNA-seq analysisoverview

    Mapping&Geneexpressionestimate

    Rawdata:fastq files

    • Cellranger (10x)• Dropseq - Alevin/Kallisto Bustools

    (transcriptomeonly)• Dropletutils• nf-core/scrnaseq• ….

  • scRNA-seq analysisoverview

    Mapping&Geneexpressionestimate

    QC:RemovelowQcells

    Removecontaminants

    Rawdata:fastq files

    • Low/highnumberofreads• Low/highnumberofgenes• Intronic reads• Mitochondrialcontent• Mappingstats• …

  • scRNA-seq analysisoverview

    Mapping&Geneexpressionestimate

    QC:RemovelowQcells

    Removecontaminants

    Data:Expressionprofiles

    Rawdata:fastq files

    • Datanormalization• Genesetselection• Batcheffectremoval• Removalofother

    confounders

  • scRNA-seq analysisoverview

    Mapping&Geneexpressionestimate

    QC:RemovelowQcells

    Removecontaminants

    Data:Expressionprofiles

    Rawdata:fastq files

    • Datanormalization• Genesetselection• Batcheffectremoval• Removalofother

    confounders

    Visualization/Dimensionalityreduction

    • PCA/ICA/MDS• tSNE• UMAP• Diffusionmaps• …

  • scRNA-seq analysisoverview

    Mapping&Geneexpressionestimate

    QC:RemovelowQcells

    Removecontaminants

    Data:Expressionprofiles

    Rawdata:fastq files

    Definingcelltypes/lineages

    • Clusteringmethods

    • Trajectoryassignment

    • Datanormalization• Genesetselection• Batcheffectremoval• Removalofother

    confounders

    Visualization/Dimensionalityreduction

  • scRNA-seq analysisoverview

    Mapping&Geneexpressionestimate

    QC:RemovelowQcells

    Removecontaminants

    Data:Expressionprofiles

    Rawdata:fastq files

    Definingcelltypes/lineages

    Genesignatures

    • Clusteringmethods

    • Trajectoryassignment

    • Datanormalization• Genesetselection• Batcheffectremoval• Removalofother

    confounders

    Visualization/Dimensionalityreduction

  • scRNA-seq analysisoverview

    Mapping&Geneexpressionestimate

    QC:RemovelowQcells

    Removecontaminants

    Data:Expressionprofiles

    Rawdata:fastq files

    Definingcelltypes/lineages

    Genesignatures

    Verificationexperiments

    • Clusteringmethods

    • Trajectoryassignment

    • Datanormalization• Genesetselection• Batcheffectremoval• Removalofother

    confounders

    Visualization/Dimensionalityreduction

  • Manyavailabletoolsforanalysis

    https://www.scrna-tools.org/

  • Inthiscourse

    • Wehaveselectedasetoftools/pipelinesthatwethinkarerelevantformostcases.

    • Cannotcoveralltoolsthatareoutthere.• Useyourcommonsensetoselectmethodsforyourproblem.

  • Coursecontent

    • Monday:scMethodology,QC• Tuesday:Normalization,Dimensionalityreduction,Batchcorrection

    • Wednesday:Clustering,Differentialexpression• Thursday:Trajectoryinference,Spatialtransciptomics• Friday:Celltype prediction,Multimodalomics.Coursesummary.


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