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Geuvadis WP4: RNAseq Analysis plans and practicalities

Geuvadis WP4: RNAseq Analysis plans and practicalities. Tuuli Lappalainen University of Geneva. Geuvadis Analysis Group Meeting, April 17, 2012, Geneva. The next months of analysis. pre-CSHL : first round of analysis to show that we have a great dataset

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Geuvadis WP4: RNAseq Analysis plans and practicalities

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  1. Geuvadis WP4: RNAseqAnalysis plans and practicalities Tuuli Lappalainen University of Geneva Geuvadis Analysis Group Meeting, April 17, 2012, Geneva

  2. The next months of analysis • pre-CSHL : first round of analysis to show that • we have a great dataset • we can analyze many cool aspects of transcriptome variation • post-CSHL : analysis aiming for the paper • final QC to freeze a really clean dataset • analysis: • some but not overly exhaustive exploration on methods, no reinvention of wheels. • start from things that we can already to well or have methods for • proceed to more complex things progressively • if some lines of analysis opens up a lot, there’s always a possibility to start building companion papers

  3. Biology of Genomes poster @ CSHL • project description • data quality: replicate samples PCA, etc • Genetic distance / ASE distance / expression distance • eQTLs and their overlap with functional elements • transcriptome qualitative/quantitative variation • sQTLs • UTR length variation or other n-TARs? • something about miRNAs… • LoFs – Manny’s plots, other things? • Epistasis from ASE

  4. Analysis breakdown Main paper focused on biology 1.1 Data production in a multicenter scheme Olof, Jonas, Natalja, Micha, Tuuli… 1.2 miRNA QC Marc F,Natalja, Esther 2. SNP calling from RNAseq data – not from technical perspective, RNA editing aspects, important also in LoF Thomas W, Thomas S, Tim, Micha… 3. Detection of splice junctions & mechanisms. Enriching annotation. Splice variation in populations  link to genetic variation and eQTLs. “Every individual has X number of unique splice variants”. Micha, Rob, Matthias, Peter, Irina, Pedro… 4. Novel transcriptional active regions, UTR length.Population variation in this -> link to genetic variation (similarly to splice junctions). Biases in annotation (population, variant frequency, variant replicability) Think about shortening of UTRs too. Rob, Matthias, Micha 5. Transcript ratio variation. Jean, Pedro 6. miRNA variation, quantitative and qualitative, effects of variants in miRNAs Marc F, Peter, Natalja, Esther 7. miRNA – target interactions Marc F, Rob, Peter, Natalja, Esther 8. rQTLs (expr variation & level, splicing, UTR length, miRNA, miRNA targets) and functional annotation of the variants How much of variation is explained by genetics, at least a lower boundary. How much of allelic effects is captured by eQTLs What kind of genes have lots of variation that we can or can not explain by genetic variants that we find. Join model of different types of QTLs TSS start sites too. Tuuli (with input from 4, 5, 6), Thomas W & S, Micha 9. Structural variant effects on transcription (cis and trans), transcript structures Tuuli, Peter, Kai Ye 10. Rare regulatory variants ASE approaches Tuuli 11. Loss-of-function variants. Functional effects of old annotated LOFs, Characterization of new putative LoFs (especially splice sites. In a quantitative manner). Link to common variation. Efficiency of NMD. Input from 4 and 7) Manny, Micha, Tuuli, Daniel, Thomas W & S… 12. Visualization and data sharing Natalja Last. Global quantitative/qualitative variation Pathway aspects – what kinds of genes (in terms on ontologies, conservation) have low-high quantitative and/or qualitative variaton. Individual similarity: genetic - allelic - expression level – transcript level – splice variants. Estimating how much is genetic – maybe also locally (genetic similarity of a region vs transcript similarty).

  5. Communication and data sharing • Wiki • will contain full documentation of the basic datasets (mapping, quantification, genotypes) • all presentations should be uploaded to the wiki. Feel free to include additional information too • FTP • needs a bit of cleaning right now – to be done this week (Tuuli & Natalja). • a separate folder for temporary file transfers • when you’ve downloaded data for common use, send an email to the analysis list • TCs • calls every week? • Skype • I’m pretty much always online. Feel free to drop a line anytime if there’s anything

  6. Next analysis group meeting in June/JulyBarcelona

  7. Action items • Tuuli/Natalja: organize ftp, send an email of the current status • Tuuli, Micha/Thasso/Paolo: update wiki • Marc S: look at 15-mers in the Berlin mRNA libraries • Tuuli, Marc F: include miRNA targets in the variant annotation • Marc F, Peter: updates to miRNA pipeline • Tuuli will prepare a summary for the whole RNAseq group TC • everyone: analysis as discussed

  8. The consortium UNIGE (Geneva) Manolis Dermitzakis StylianosAntonarakis Tuuli Lappalainen Thomas Giger Emilie Falconnet Luciana Romano Alexandra Planchon IsmaelPadioleau Alisa Yurovsky CRG/CNAG/USC (Barcelona) Xavier Estivill Ivo Gut RodericGuigo Angel Carracedo Alvarez Gabrielle Bertier MichaSammeth ThassoGriber Paolo Ribeca Pedro Ferreira Jean Monlong Esther Lizano Marc Friedländer Marta Gut SergiBertranAgullo ICMB (Kiel) Stefan Schreiber Philip Rosenstiel Matthias Barann MPIMG (Berlin) Hans Lehrach Ralf Sudbrak Marc Sultan VyacheslavAmstislavskiy LUMC (Leiden) Gert-Jan van Ommen Peter ‘tHoen Irina Pulyakhina UU (Uppsala) Ann-Christine Syvänen OlofKarlberg Jonas Almlöf Mathias Brännvall HMGU (Munich) Thomas Meitinger Tim Strom Thomas Wieland Thomas Schwarzmayr EBI AlvisBrazma NataljaKurbatova Oxford University Manuel Rivas Massachusetts General Hospital Daniel McArthur ECACC Bryan Bolton Karen Ball Edward Burnett Jim Cooper Who is missing??

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