FISH546 Discussion4

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The document appears to be notes from a discussion on next generation sequencing techniques and data analysis. It covers topics like DNA sequencing using beads, ligation, colorspace encoding, assembling short read sequences, working with raw sequencing data files, and storing and managing the large amounts of data generated from sequencing.

Technology News & Politics

Discussion 4

•>
• SAFS INquiry
• assembly / LDS

Tuesday, January 26, 2010 1

ABI SOLiD (in depth)

Tuesday, January 26, 2010 2

DNA on a bead

Tuesday, January 26, 2010 3

*
A M J J A S O N D J F M A M

Tuesday, January 26, 2010 10

Transcriptomics

16 million
~40 bp
HQ reads

16 million
~40 bp
HQ reads

Tuesday, January 26, 2010 13

dealing with raw data

Tuesday, January 26, 2010 20

dealing with raw data

Tuesday, January 26, 2010 21

dealing with raw data

Tuesday, January 26, 2010 22

dealing with raw data

Tuesday, January 26, 2010 23

dealing with raw data

Tuesday, January 26, 2010 24

dealing with raw data

Tuesday, January 26, 2010 25

dealing with raw data $$$$$$

Tuesday, January 26, 2010 26

dealing with raw data $$$$$$

Tuesday, January 26, 2010 27

dealing with raw data

Tuesday, January 26, 2010 28

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

ESTs Short Reads (ngs)

Tuesday, January 26, 2010 31

ESTs Short Reads (ngs)

options:
assemble (non-redundant)
Blast Separately
Assemble on Reference (MAP/Variant)
Assemble on Reference (RNAseq)

Tuesday, January 26, 2010 32

ESTs

Assembly

Tuesday, January 26, 2010 33

ngs

Assembly

Tuesday, January 26, 2010 34

ngs - assembly open source

de novo

Tuesday, January 26, 2010 35

ngs - assembly $$$

Tuesday, January 26, 2010 36

ngs - assembly

Tuesday, January 26, 2010 37

ngs - assembly

Tuesday, January 26, 2010 38

ngs - assembly

Tuesday, January 26, 2010 39

ngs - assembly

Tuesday, January 26, 2010 40

ngs - assembly

Tuesday, January 26, 2010 41

ngs - assembly

Tuesday, January 26, 2010 42

ngs - assembly

9:39

Tuesday, January 26, 2010 43

ngs - assembly

10:00

Tuesday, January 26, 2010 44

assemble ngs cell

Tuesday, January 26, 2010 51

assemble ngs cell

Tuesday, January 26, 2010 52

assemble ngs cell

Tuesday, January 26, 2010 53

output = consensus

Tuesday, January 26, 2010 54

output = consensus

ESTs ngs

Tuesday, January 26, 2010 55

output = consensus

ESTs ngs

Tuesday, January 26, 2010 56

annotation

Tuesday, January 26, 2010 58

annotation

Tuesday, January 26, 2010 59

annotation

Tuesday, January 26, 2010 60

annotation

Tuesday, January 26, 2010 61

annotation

Tuesday, January 26, 2010 62

data management

relational databases

very large ﬁles

Tuesday, January 26, 2010 73

data management

Tuesday, January 26, 2010 74

data management

Tuesday, January 26, 2010 75

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FISH546 Discussion4

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