Dinh/NOTES/2010-8-2

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BC Data[edit]

RUN Data file Total Reads Reads Mapped %Mapped
100707_VCU.s6 – B11 05359A17-2.txt.fwd.soap.out 26397645 9449382 73.30%
05359A17-2.txt.rev.soap.out 26397645 9899692
100707_VCU.s7 – B12 05359B09-2.txt.fwd.soap.out 22561783 7448390 67.46%
05359B09-2.txt.rev.soap.out 22561783 7771943
100707_VCU.s8 – B13 07292A17-2.txt.fwd.soap.out 21651217 7316786 69.74%
07292A17-2.txt.rev.soap.out 21651217 7782123
100707_VCU.s5 – B28 13066B09-2.txt.fwd.soap.out 5878199 2266706 73.64%
13066B09-2.txt.rev.soap.out 5878199 2061829
HL066.s2 - B10 05215B09-3.txt.fwd.soap.out 18662642 7877191 78.75%
05215B09-3.txt.rev.soap.out 18662642 6819577
sample Total CpGs >10 Average Read depth
05359A17-2 122417 43.5217085862258
05359B09-2 104734 38.9330876315237
07292A17-2 112793 39.872039931556
13066B09-2 45511 20.0854958141988
05215B09-2 98136 34.386565582457

File:Hcorcluster-4 bc hc matrix.png

5_bc_matrix.txt[edit]

  1. Combine 13066B09 and 12066B09-2
  2. Combine 05215B09 and 05215B09-2
  3. Replace 07292A17, 05359B09, and 05349A17 with new sequence data (version -2).

File:Hcorcluster-5 bc hc matrix.png

Data Summary[edit]

Sample CpG with >=10 reads depth Average reads depth
01192B09 118833 57
01230B09 105296 61
01373A17 140926 56
01373B09 103324 35
01436B09 180997 100
01523B09 169311 113
03170B09 129564 140
03259B09 111084 54
05192A18 93893 54
05192B09 86800 48
05215A18 83654 38
05215B09 106225 48
05359A17 122417 44
05359B09 104734 39
07292A17 112793 40
07292B09 99666 37
09075B09 131702 115
09092B09 80474 60
09123A17 93156 83
09123B09 102562 73
09206B09 101448 63
09265B09 112117 75
09351A17 106208 74
09351B09 95911 68
09491A17 102754 77
09491B09 97963 85
11306A18 99406 89
11306B09 97324 88
13066A17 101925 90
13066B09 64148 41