20120423.NGS.Rennes

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My presentation about Knime4Bio.

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20120423.NGS.Rennes

  1. 1. Knime4Bio a set of custom nodes for the interpretation of NGS data with KNIME. Biogenouest Génomique Rennes 23 avril 2012 Pierre Lindenbaum PhD UMR1087 – Institut du thorax @yokofakunhttp://plindenbaum.blogspot.com
  2. 2. http://commons.wikimedia.org/wiki/File:Calendar-leapyeardate.jpg
  3. 3. http://www.nature.com/news/2011/111005/full/478022a/box/1.html
  4. 4. VCFhttp://bioinf.comav.upv.es/courses/sequence_analysis/snp_calling.html
  5. 5. How do weanalyze/filterthose data ?
  6. 6. Command line Line Command
  7. 7. grep ­v "PATH" < sample2vcf.tsv |${VARKIT}/scanvcf |${VARKIT}/normalizechrom | Command lineawk ­F   ($3==".") |sort ­t   ­k1,1 ­k2,2n ­k4,4 ­k5,5 ­k11,11 |${VARKIT}/samplespersnp ­­sample 11 |awk ­F   ($12=="1") |${VARKIT}/extractinfo ­t DP |${VARKIT}/extractinfo ­t GN |${VARKIT}/extractinfo ­t PRED |${VARKIT}/extractformat ­t GT |awk ­F   (int($6)>25.0) |awk ­F   (int($13)>10.0) |awk ­F   ($16!="1/1") |awk ­F   ($15!="EXON_SYNONYMOUS" && $15!="GENOMIC" && $15!="INTRON") |groupbygene ­­gene 14 ­­sample 11 |awk ­F   (int($5)==2) |awk ­F   (int($6)==2)
  8. 8. http://code.google.com/p/variationtoolkit/
  9. 9. “command line”A PhD candidate
  10. 10. Did you includeDid we try fix the the results from maximum Polyphen ?number of SNPs per gene ? Can you test with a minimal DEPTH=20 ? Did we ever find this gene ? And with minimal number of affected samples per SNP = 2 ? And with minimal number of affected Can you removesamples per gene = 4 ? all the known SNPs ?
  11. 11. http://www.flickr.com/photos/ohm17/162622755
  12. 12. I want a GUI
  13. 13. http://research.nhgri.nih.gov/software/VarSifter/
  14. 14. Apache Tomcatservlets/jsp SAM-JDK
  15. 15. Java Swing (GUI) based solution
  16. 16. A quick access to the data was needed.http://www.oracle.com/technetwork/database/berkeleydb/overview/index-093405.html
  17. 17. WORKFLOW ENGINE
  18. 18. http://mobyle.pasteur.fr/
  19. 19. http://main.g2.bx.psu.edu/ Galaxy
  20. 20. TAVERNA http://www.taverna.org.uk/
  21. 21. http://en.wikipedia.org/wiki/File:Knime.jpg
  22. 22. http://www.flickr.com/photos/knolleary/6212065238
  23. 23. http://code.google.com/p/knime4bio/
  24. 24. NCBI Entrez
  25. 25. Intersections BED UCSC TABIX bigwig …
  26. 26. WEB SERVICES EMBL STRINGExome Variant Server UNIPROT DAS ….
  27. 27. PREDICTIONS SnpEFFBasic Predictions ….
  28. 28. Interaction with the Client IGVReading the BAM ….
  29. 29. NCBI Protein
  30. 30. Java snippet
  31. 31. Tabix
  32. 32. Uniprot
  33. 33. Implementing a new node is easy
  34. 34. interface Model { Table[] execute(Table tables[]); }
  35. 35. MerciVincent PorteroChristian DinaEstelle BaronStephanie ChatelMarta SanchezStéphanie BonnaudMatilde KarakachoffRichard RedonHadja EldjouziFrançoise GrosAurore DespresLaetitia DuboscqEric CharpentierSimon LecointeFlogiane SimoretSolena le ScouarnecThe Biostar community

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