Discussion 4


                   •>
                   • SAFS INquiry
                   • assembly / LDS




Tuesday, Ja...
ABI SOLiD (in depth)




Tuesday, January 26, 2010                     2
DNA on a bead




Tuesday, January 26, 2010                   3
Ligation




Tuesday, January 26, 2010              4
colorspace




Tuesday, January 26, 2010                5
colorspace




Tuesday, January 26, 2010                6
case study




Tuesday, January 26, 2010   7
Tuesday, January 26, 2010   8
Tuesday, January 26, 2010   9
*
                            A M J J A S O N D J F M A M




Tuesday, January 26, 2010                                 10
Tuesday, January 26, 2010   11
Tuesday, January 26, 2010   12
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      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
   r...
now what?




Tuesday, January 26, 2010   30
ESTs        Short Reads (ngs)




Tuesday, January 26, 2010                       31
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




Tuesday, January 26, 2010   54
output = consensus


                  ESTs      ngs




Tuesday, January 26, 2010         55
output = consensus


                  ESTs      ngs




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




                        options:
                        assemble (non...
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
default




Tuesday, January 26, 2010   63
default




Tuesday, January 26, 2010   64
changes




Tuesday, January 26, 2010   65
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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FISH546 Discussion4

  1. 1. Discussion 4 •> • SAFS INquiry • assembly / LDS Tuesday, January 26, 2010 1
  2. 2. ABI SOLiD (in depth) Tuesday, January 26, 2010 2
  3. 3. DNA on a bead Tuesday, January 26, 2010 3
  4. 4. Ligation Tuesday, January 26, 2010 4
  5. 5. colorspace Tuesday, January 26, 2010 5
  6. 6. colorspace Tuesday, January 26, 2010 6
  7. 7. case study Tuesday, January 26, 2010 7
  8. 8. Tuesday, January 26, 2010 8
  9. 9. Tuesday, January 26, 2010 9
  10. 10. * A M J J A S O N D J F M A M Tuesday, January 26, 2010 10
  11. 11. Tuesday, January 26, 2010 11
  12. 12. Tuesday, January 26, 2010 12
  13. 13. Transcriptomics 16 million ~40 bp HQ reads 16 million ~40 bp HQ reads Tuesday, January 26, 2010 13
  14. 14. raw data Tuesday, January 26, 2010 14
  15. 15. csfasta Tuesday, January 26, 2010 15
  16. 16. csfasta Tuesday, January 26, 2010 16
  17. 17. csfasta Tuesday, January 26, 2010 17
  18. 18. qual Tuesday, January 26, 2010 18
  19. 19. stats Tuesday, January 26, 2010 19
  20. 20. dealing with raw data Tuesday, January 26, 2010 20
  21. 21. dealing with raw data Tuesday, January 26, 2010 21
  22. 22. dealing with raw data Tuesday, January 26, 2010 22
  23. 23. dealing with raw data Tuesday, January 26, 2010 23
  24. 24. dealing with raw data Tuesday, January 26, 2010 24
  25. 25. dealing with raw data Tuesday, January 26, 2010 25
  26. 26. dealing with raw data $$$$$$ Tuesday, January 26, 2010 26
  27. 27. dealing with raw data $$$$$$ Tuesday, January 26, 2010 27
  28. 28. dealing with raw data Tuesday, January 26, 2010 28
  29. 29. trimmed Processed a total of 43490590 sequences. 27309944 sequences have been completely removed during trimming. 1190442453 nucleotides have been trimmed, altogether. Tuesday, January 26, 2010 29
  30. 30. now what? Tuesday, January 26, 2010 30
  31. 31. ESTs Short Reads (ngs) Tuesday, January 26, 2010 31
  32. 32. ESTs Short Reads (ngs) options: assemble (non-redundant) Blast Separately Assemble on Reference (MAP/Variant) Assemble on Reference (RNAseq) Tuesday, January 26, 2010 32
  33. 33. ESTs Assembly Tuesday, January 26, 2010 33
  34. 34. ngs Assembly Tuesday, January 26, 2010 34
  35. 35. ngs - assembly open source de novo Tuesday, January 26, 2010 35
  36. 36. ngs - assembly $$$ Tuesday, January 26, 2010 36
  37. 37. ngs - assembly Tuesday, January 26, 2010 37
  38. 38. ngs - assembly Tuesday, January 26, 2010 38
  39. 39. ngs - assembly Tuesday, January 26, 2010 39
  40. 40. ngs - assembly Tuesday, January 26, 2010 40
  41. 41. ngs - assembly Tuesday, January 26, 2010 41
  42. 42. ngs - assembly Tuesday, January 26, 2010 42
  43. 43. ngs - assembly 9:39 Tuesday, January 26, 2010 43
  44. 44. ngs - assembly 10:00 Tuesday, January 26, 2010 44
  45. 45. assemble Tuesday, January 26, 2010 45
  46. 46. Tuesday, January 26, 2010 46
  47. 47. Tuesday, January 26, 2010 47
  48. 48. Tuesday, January 26, 2010 48
  49. 49. Tuesday, January 26, 2010 49
  50. 50. Tuesday, January 26, 2010 50
  51. 51. assemble ngs cell Tuesday, January 26, 2010 51
  52. 52. assemble ngs cell Tuesday, January 26, 2010 52
  53. 53. assemble ngs cell Tuesday, January 26, 2010 53
  54. 54. output = consensus Tuesday, January 26, 2010 54
  55. 55. output = consensus ESTs ngs Tuesday, January 26, 2010 55
  56. 56. output = consensus ESTs ngs Tuesday, January 26, 2010 56
  57. 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. 58. annotation Tuesday, January 26, 2010 58
  59. 59. annotation Tuesday, January 26, 2010 59
  60. 60. annotation Tuesday, January 26, 2010 60
  61. 61. annotation Tuesday, January 26, 2010 61
  62. 62. annotation Tuesday, January 26, 2010 62
  63. 63. default Tuesday, January 26, 2010 63
  64. 64. default Tuesday, January 26, 2010 64
  65. 65. changes Tuesday, January 26, 2010 65
  66. 66. changes Tuesday, January 26, 2010 66
  67. 67. Tuesday, January 26, 2010 67
  68. 68. Tuesday, January 26, 2010 68
  69. 69. Tuesday, January 26, 2010 69
  70. 70. Tuesday, January 26, 2010 70
  71. 71. Tuesday, January 26, 2010 71
  72. 72. Tuesday, January 26, 2010 72
  73. 73. data management relational databases very large files Tuesday, January 26, 2010 73
  74. 74. data management Tuesday, January 26, 2010 74
  75. 75. data management Tuesday, January 26, 2010 75
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