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FISH546 Discussion4

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  • 1. Discussion 4 •> • SAFS INquiry • assembly / LDS Tuesday, January 26, 2010 1
  • 2. ABI SOLiD (in depth) Tuesday, January 26, 2010 2
  • 3. DNA on a bead Tuesday, January 26, 2010 3
  • 4. Ligation Tuesday, January 26, 2010 4
  • 5. colorspace Tuesday, January 26, 2010 5
  • 6. colorspace Tuesday, January 26, 2010 6
  • 7. case study Tuesday, January 26, 2010 7
  • 8. Tuesday, January 26, 2010 8
  • 9. Tuesday, January 26, 2010 9
  • 10. * A M J J A S O N D J F M A M Tuesday, January 26, 2010 10
  • 11. Tuesday, January 26, 2010 11
  • 12. Tuesday, January 26, 2010 12
  • 13. Transcriptomics 16 million ~40 bp HQ reads 16 million ~40 bp HQ reads Tuesday, January 26, 2010 13
  • 14. raw data Tuesday, January 26, 2010 14
  • 15. csfasta Tuesday, January 26, 2010 15
  • 16. csfasta Tuesday, January 26, 2010 16
  • 17. csfasta Tuesday, January 26, 2010 17
  • 18. qual Tuesday, January 26, 2010 18
  • 19. stats Tuesday, January 26, 2010 19
  • 20. dealing with raw data Tuesday, January 26, 2010 20
  • 21. dealing with raw data Tuesday, January 26, 2010 21
  • 22. dealing with raw data Tuesday, January 26, 2010 22
  • 23. dealing with raw data Tuesday, January 26, 2010 23
  • 24. dealing with raw data Tuesday, January 26, 2010 24
  • 25. dealing with raw data Tuesday, January 26, 2010 25
  • 26. dealing with raw data $$$$$$ Tuesday, January 26, 2010 26
  • 27. dealing with raw data $$$$$$ Tuesday, January 26, 2010 27
  • 28. dealing with raw data Tuesday, January 26, 2010 28
  • 29. trimmed Processed a total of 43490590 sequences. 27309944 sequences have been completely removed during trimming. 1190442453 nucleotides have been trimmed, altogether. Tuesday, January 26, 2010 29
  • 30. now what? Tuesday, January 26, 2010 30
  • 31. ESTs Short Reads (ngs) Tuesday, January 26, 2010 31
  • 32. ESTs Short Reads (ngs) options: assemble (non-redundant) Blast Separately Assemble on Reference (MAP/Variant) Assemble on Reference (RNAseq) Tuesday, January 26, 2010 32
  • 33. ESTs Assembly Tuesday, January 26, 2010 33
  • 34. ngs Assembly Tuesday, January 26, 2010 34
  • 35. ngs - assembly open source de novo Tuesday, January 26, 2010 35
  • 36. ngs - assembly $$$ Tuesday, January 26, 2010 36
  • 37. ngs - assembly Tuesday, January 26, 2010 37
  • 38. ngs - assembly Tuesday, January 26, 2010 38
  • 39. ngs - assembly Tuesday, January 26, 2010 39
  • 40. ngs - assembly Tuesday, January 26, 2010 40
  • 41. ngs - assembly Tuesday, January 26, 2010 41
  • 42. ngs - assembly Tuesday, January 26, 2010 42
  • 43. ngs - assembly 9:39 Tuesday, January 26, 2010 43
  • 44. ngs - assembly 10:00 Tuesday, January 26, 2010 44
  • 45. assemble Tuesday, January 26, 2010 45
  • 46. Tuesday, January 26, 2010 46
  • 47. Tuesday, January 26, 2010 47
  • 48. Tuesday, January 26, 2010 48
  • 49. Tuesday, January 26, 2010 49
  • 50. Tuesday, January 26, 2010 50
  • 51. assemble ngs cell Tuesday, January 26, 2010 51
  • 52. assemble ngs cell Tuesday, January 26, 2010 52
  • 53. assemble ngs cell Tuesday, January 26, 2010 53
  • 54. output = consensus Tuesday, January 26, 2010 54
  • 55. output = consensus ESTs ngs Tuesday, January 26, 2010 55
  • 56. output = consensus ESTs ngs Tuesday, January 26, 2010 56
  • 57. ESTs Short Reads (ngs) options: assemble (non-redundant) Blast Separately Assemble on Reference (MAP/Variant) Assemble on Reference (RNAseq) Tuesday, January 26, 2010 57
  • 58. annotation Tuesday, January 26, 2010 58
  • 59. annotation Tuesday, January 26, 2010 59
  • 60. annotation Tuesday, January 26, 2010 60
  • 61. annotation Tuesday, January 26, 2010 61
  • 62. annotation Tuesday, January 26, 2010 62
  • 63. default Tuesday, January 26, 2010 63
  • 64. default Tuesday, January 26, 2010 64
  • 65. changes Tuesday, January 26, 2010 65
  • 66. changes Tuesday, January 26, 2010 66
  • 67. Tuesday, January 26, 2010 67
  • 68. Tuesday, January 26, 2010 68
  • 69. Tuesday, January 26, 2010 69
  • 70. Tuesday, January 26, 2010 70
  • 71. Tuesday, January 26, 2010 71
  • 72. Tuesday, January 26, 2010 72
  • 73. data management relational databases very large files Tuesday, January 26, 2010 73
  • 74. data management Tuesday, January 26, 2010 74
  • 75. data management Tuesday, January 26, 2010 75