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