0
Transcriptomics


                            16 million
                              ~40 bp
                            ...
raw data




Tuesday, January 26, 2010   14
csfasta




Tuesday, January 26, 2010   15
csfasta




Tuesday, January 26, 2010   16
csfasta




Tuesday, January 26, 2010   17
qual




Tuesday, January 26, 2010   18
stats




Tuesday, January 26, 2010   19
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
   r...
ESTs                          Short Reads (ngs)




                        options:
                        assemble (non...
ESTs

                            Assembly




Tuesday, January 26, 2010              33
ngs

                            Assembly




Tuesday, January 26, 2010              34
ngs - assembly                 open source

                            de novo




Tuesday, January 26, 2010             ...
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




Tuesday, January 26, 2010   45
Tuesday, January 26, 2010   46
Tuesday, January 26, 2010   47
Tuesday, January 26, 2010   48
Tuesday, January 26, 2010   49
Tuesday, January 26, 2010   50
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


                  ESTs      ngs




Tuesday, January 26, 2010         56
ESTs                          Short Reads (ngs)




                        options:
                        assemble (non...
annotation




Tuesday, January 26, 2010   59
annotation




Tuesday, January 26, 2010   60
annotation




Tuesday, January 26, 2010   61
annotation




Tuesday, January 26, 2010   62
default




Tuesday, January 26, 2010   64
changes




Tuesday, January 26, 2010   66
Tuesday, January 26, 2010   67
Tuesday, January 26, 2010   68
Tuesday, January 26, 2010   69
Tuesday, January 26, 2010   70
Tuesday, January 26, 2010   71
Tuesday, January 26, 2010   72
data management


                            relational databases


                                          very large ...
data management




Tuesday, January 26, 2010   74
data management




Tuesday, January 26, 2010   75
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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

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Transcript of "FISH546 Discussion4"

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