次世代シーケンサのデータ解析 技術開発編

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  • 1. 2011/03/18 AJACS 8 id:mickey242011 3 18
  • 2. id: mickey24 (@mickey24)2011 3 18
  • 3. • DBCLS RA 2009/05 •2011 3 18
  • 4. NGS2011 3 18
  • 5. • gmap • togofarm bot2011 3 18
  • 6. gmap NGS for Sun Grid Engine2011 3 18
  • 7. NGS • • DNA • TopHat - Bowtie Cufflinks2011 3 18
  • 8. DBCLS • RA NGS • 8CPU RAM 16GB ×8 • (Sun Grid Engine)2011 3 18
  • 9. 24 … 1 … ! " # $ % &&& "! "" ( 24 … ! " # $ % &&& "! "" ( ( )2011 3 18
  • 10. Sun Grid Engine • qsub $ qsub [qsub ] [ ] • qsub • • • •2011 3 18
  • 11. Sun Grid Engine NGS … • • •2011 3 18
  • 12. $ qsub submit_tophat_job.sh [ ] /path/to/genome/mouse /path/to/SRP000198/SRX000351/SRR001360.fastq Your job 723552 ("foo") has been submitted $ qstat -u mickey $ less /path/to/qsub_log ( ) NG!2011 3 18
  • 13. vs /path/to/SRP000198/SRX000351/SRR001360.fastq with vs /path/to/SRP000198/SRX000351/SRR001361.fastq with vs /path/to/SRP000230/SRX000436/SRR002010.fastq with vs /path/to/SRP001050/SRX002424/SRR003361.fastq with • … → → NG!2011 3 18
  • 14. … gmap2011 3 18
  • 15. gmap • NGS • Sun Grid Engine • RA • • TopHat • Bowtie • SOAP22011 3 18
  • 16. GitHub https://github.com/mickey24/gmap2011 3 18
  • 17. gmap • • gmap • • • • COOL!2011 3 18
  • 18. # ruby_path : /path/to/ruby qsub_path : /path/to/qsub tophat_path : /path/to/tophat bowtie_path : /path/to/bowtie ( ) # genome_config: mouse: genome_path : /path/to/genome/mouse/%s chrnum : 1-19,X,Y # (SRP) project_config: SRP000198: tophat : "--solexa-quals -r 200 --mate-std-dev 50" bowtie : "-X 250 -I 150" soap2 : "-x 250 -m 150"2011 3 18
  • 19. gmap @DBCLS gmap !"#$ $ gmap -t tophat -g mouse /path/to/reads.fastq qsub2011 3 18
  • 20. gmap $ gmap -t tophat -g mouse /path/to/SRP000198/SRX000351/SRR001360.fastq tool name : tophat genome index : mouse input file : /path/to/SRP000198/SRX000351/SRR001360.fastq output dir : /path/to/result/SRP000198/SRX000351/SRR001360/tophat project config : SRP000198 chrnum : 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y submit jobs? (y/n) y Your job 723552 ("mt_1") has been submitted Your job 723553 ("mt_2") has been submitted Your job 723554 ("mt_3") has been submitted ... Your job 723570 ("mt_19") has been submitted Your job 723571 ("mt_X") has been submitted Your job 723572 ("mt_Y") has been submitted finish2011 3 18
  • 21. • gmap • togofarm bot2011 3 18
  • 22. togofarm bot Twitter bot2011 3 18
  • 23. NGS • gmap … • qstat • …2011 3 18
  • 24. By the way…2011 3 18
  • 25. Twitter • …2011 3 18
  • 26. …2011 3 18
  • 27. 2011 3 18
  • 28. Twitter bot • Twitter • Twitter bot • • • •2011 3 18
  • 29. ……2011 3 18
  • 30. … togofarm bot2011 3 18
  • 31. togofarm bot • DBCLS bot • protected2011 3 18
  • 32. togofarm bot2011 3 18
  • 33. togofarm bot2011 3 18
  • 34. togofarm bot • • • •2011 3 18
  • 35. $ gmap -t tophat -g mouse /path/to/reads.fastq2011 3 18
  • 36. 2011 3 18
  • 37. 2011 3 18
  • 38. 2011 3 18
  • 39. @DBCLS !"#"$%&()"!( ( Twitter2011 3 18
  • 40. • gmap NGS ( 24 ) • Twitter ( 24 ) • qstat ( 24 ) • bot ( 24 ) • ( 24 )2011 3 18
  • 41. 2011 3 18
  • 42. g86.dbcls.jp • DBCLS RA Mac Pro • RA Web •2011 3 18
  • 43. body3d • DBCLS BodyParts3D Twitter bot • http://twitter.com/body3d • http://g86.dbcls.jp/~body3d/2011 3 18
  • 44. body3d2011 3 18
  • 45. 2011 3 18
  • 46. • NGS • gmap • NGS for Sun Grid Engine • togofarm bot • Twitter bot2011 3 18
  • 47. • • • •2011 3 18
  • 48. •2 • @bonohu • @chalkless • @h_ono • • DBCLS2011 3 18
  • 49. 2011 3 18