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

1. Transcriptomics
16 million
~40 bp
HQ reads
16 million
~40 bp
HQ reads
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2. raw data
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3. csfasta
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4. csfasta
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5. csfasta
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6. qual
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7. stats
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8. dealing with raw data
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9. dealing with raw data
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10. dealing with raw data
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11. dealing with raw data
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12. dealing with raw data
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13. dealing with raw data $$$$$$
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14. dealing with raw data $$$$$$
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15. dealing with raw data
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16. trimmed
Processed a total of
43490590
sequences.
27309944
sequences have
been completely
removed during
trimming.
1190442453
nucleotides have
been trimmed,
altogether.
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17. ESTs Short Reads (ngs)
options:
assemble (non-redundant)
Blast Separately
Assemble on Reference (MAP/Variant)
Assemble on Reference (RNAseq)
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18. ESTs
Assembly
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19. ngs
Assembly
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20. ngs - assembly open source
de novo
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21. ngs - assembly $$$
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22. ngs - assembly
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23. ngs - assembly
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24. ngs - assembly
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25. ngs - assembly
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26. ngs - assembly
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27. ngs - assembly
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28. ngs - assembly
9:39
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29. ngs - assembly
10:00
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30. assemble
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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
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37. assemble ngs cell
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38. assemble ngs cell
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39. output = consensus
ESTs ngs
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40. ESTs Short Reads (ngs)
options:
assemble (non-redundant)
Blast Separately
Assemble on Reference (MAP/Variant)
Assemble on Reference (RNAseq)
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41. annotation
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42. annotation
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43. annotation
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44. annotation
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45. default
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46. changes
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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
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54. data management
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55. data management
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