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.

1. Discussion 4
•>
• SAFS INquiry
• assembly / LDS
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2. ABI SOLiD (in depth)
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3. DNA on a bead
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4. Ligation
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5. colorspace
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6. colorspace
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7. case study
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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
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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
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14. raw data
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15. csfasta
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16. csfasta
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17. csfasta
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18. qual
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19. stats
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20. dealing with raw data
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21. dealing with raw data
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22. dealing with raw data
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23. dealing with raw data
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24. dealing with raw data
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25. dealing with raw data
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26. dealing with raw data $$$$$$
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27. dealing with raw data $$$$$$
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28. dealing with raw data
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29. trimmed
Processed a total of
43490590
sequences.
27309944
sequences have
been completely
removed during
trimming.
1190442453
nucleotides have
been trimmed,
altogether.
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30. now what?
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31. ESTs Short Reads (ngs)
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32. ESTs Short Reads (ngs)
options:
assemble (non-redundant)
Blast Separately
Assemble on Reference (MAP/Variant)
Assemble on Reference (RNAseq)
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33. ESTs
Assembly
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34. ngs
Assembly
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35. ngs - assembly open source
de novo
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36. ngs - assembly $$$
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37. ngs - assembly
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38. ngs - assembly
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39. ngs - assembly
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40. ngs - assembly
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41. ngs - assembly
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42. ngs - assembly
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43. ngs - assembly
9:39
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44. ngs - assembly
10:00
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45. assemble
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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
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52. assemble ngs cell
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53. assemble ngs cell
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54. output = consensus
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55. output = consensus
ESTs ngs
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56. output = consensus
ESTs ngs
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57. ESTs Short Reads (ngs)
options:
assemble (non-redundant)
Blast Separately
Assemble on Reference (MAP/Variant)
Assemble on Reference (RNAseq)
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58. annotation
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59. annotation
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60. annotation
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61. annotation
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62. annotation
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63. default
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64. default
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65. changes
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66. changes
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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
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74. data management
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75. data management
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