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FISH546 Discussion4

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Slides from lecture that go over assembly and annotation of NGS data using local resources

Slides from lecture that go over assembly and annotation of NGS data using local resources


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Transcript

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