FISH546 Discussion4
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FISH546 Discussion4

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FISH546 Discussion4 FISH546 Discussion4 Presentation Transcript

  • 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
  • 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 HQ reads 16 million ~40 bp HQ reads Tuesday, January 26, 2010 13
  • 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 $$$$$$ Tuesday, January 26, 2010 26
  • dealing with raw data $$$$$$ Tuesday, January 26, 2010 27
  • dealing with raw data Tuesday, January 26, 2010 28
  • trimmed Processed a total of 43490590 sequences. 27309944 sequences have been completely removed during trimming. 1190442453 nucleotides have been trimmed, altogether. Tuesday, January 26, 2010 29
  • now what? Tuesday, January 26, 2010 30
  • ESTs Short Reads (ngs) Tuesday, January 26, 2010 31
  • ESTs Short Reads (ngs) options: assemble (non-redundant) Blast Separately Assemble on Reference (MAP/Variant) Assemble on Reference (RNAseq) Tuesday, January 26, 2010 32
  • ESTs Assembly Tuesday, January 26, 2010 33
  • ngs Assembly Tuesday, January 26, 2010 34
  • ngs - assembly open source de novo Tuesday, January 26, 2010 35
  • ngs - assembly $$$ 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 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-redundant) Blast Separately Assemble on Reference (MAP/Variant) Assemble on Reference (RNAseq) Tuesday, January 26, 2010 57
  • 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 files Tuesday, January 26, 2010 73
  • data management Tuesday, January 26, 2010 74
  • data management Tuesday, January 26, 2010 75