Noi/NOTES/2011-5-26

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Mapping data of HL094 run[edit]

BSPP DMR330k capture of sample from Harvard (TET), Belmonte's lab, PGP1F, PGP1iPS, HCT116, and HCT116-DKO (Library-free)[edit]

  • Note:
    • Related lab notebook: [[1]]
    • Sequencing library ID: NP-Lib_free_Ind1_24-May3 on the sample record (labeled on the tube: NP-Lib-free_TET_Sergio.Ind1-24-May3, 2011)
    • PE read 110 7 110
    • Directory: genome-miner
      • /home/kunzhang/CpgMIP/Data/HL094
      • /media/TmpStore1/Noi_scratch/HL094
    • Merged the same index from different lanes in the flow cell
    • Trim 27bp from 5' end
    • Performed SE mapping to the hg18 version of the human genome
  • Mapping data: Media:HL094_mapping data.xlsx
' ' ' read length =110bp ' ' Forward ' Reverse ' '
Sample code sample ID # of reads # of bps (# of reads x read length) # of CpG site called # of reads alignment %mapping alignment % mapping Total %mapping
T1 Scr-1 26,302,854 2,893,313,940 514,026 26,302,854 10,429,936 39.65 8,881,977 33.77 73.42
T2 Sh3513-1 31,041,074 3,414,518,140 546,957 31,041,074 12,708,257 40.94 10,845,322 34.94 75.88
T3 Sh1-1 23,618,564 2,598,042,040 435,097 23,618,564 9,746,673 41.27 8,305,177 35.16 76.43
T4 Scr-2 35,247,962 3,877,275,820 462,256 35,247,962 14,637,935 41.53 12,444,469 35.31 76.83
T5 Sh3513-2 30,796,252 3,387,587,720 484,508 30,796,252 12,734,656 41.35 10,879,699 35.33 76.68
T6 Sh1-2 33,077,862 3,638,564,820 524,056 33,077,862 13,335,878 40.32 11,283,798 34.11 74.43
T7 Mock 32,855,094 3,614,060,340 540,086 32,855,094 13,145,443 40.01 11,164,614 33.98 73.99
T8 TET2-35 33,412,058 3,675,326,380 536,203 33,412,058 13,518,845 40.46 11,426,538 34.20 74.66
T9 TET2-75 30,201,370 3,322,150,700 534,596 30,201,370 12,182,556 40.34 10,363,001 34.31 74.65
T10 HMEC-Scr 33,917,718 3,730,948,980 540,383 33,917,718 13,758,646 40.56 11,745,957 34.63 75.20
T11 HMEC-Sh3513 25,464,900 2,801,139,000 496,909 25,464,900 10,421,868 40.93 8,860,606 34.80 75.72
T12 HMEC-Sh1 27,922,894 3,071,518,340 497,216 27,922,894 11,489,193 41.15 9,785,247 35.04 76.19
S13 PGP1F 33,494,842 3,684,432,620 563,424 33,494,842 13,581,537 40.55 11,473,747 34.26 74.80
S14-1 PGP1 iPS-1 29,987,390 3,298,612,900 479,778 29,987,390 12,625,013 42.10 10,627,028 35.44 77.54
S14-2 PGP1 iPS-2 27,999,660 3,079,962,600 463,886 27,999,660 11,674,367 41.69 9,822,269 35.08 76.77
S16 hHCT116 24,951,540 2,744,669,400 496,734 24,951,540 10,387,693 41.63 8,816,603 35.33 76.97
S17 hHCT116 DKO 26,154,076 2,876,948,360 529,819 26,154,076 10,523,913 40.24 8,958,507 34.25 74.49
S18 MSCs P7 31,381,752 3,451,992,720 366,816 31,381,752 13,347,314 42.53 10,453,103 33.31 75.84
S19 MSCiPS#4 28,604,252 3,146,467,720 384,091 28,604,252 11,227,513 39.25 8,967,038 31.35 70.60
S20 MSCiPS#8 42,135,600 4,634,916,000 423,447 42,135,600 16,702,610 39.64 13,308,180 31.58 71.22
S21 H1 41,519,000 4,567,090,000 416,529 41,519,000 16,266,912 39.18 12,971,167 31.24 70.42
S22 H9 30,042,994 3,304,729,340 355,665 30,042,994 12,430,116 41.37 9,709,813 32.32 73.69
S23 cAWS1(S1-S5) 30,276,368 3,330,400,480 370,227 30,276,368 12,306,373 40.65 9,732,450 32.15 72.79
S23 cAWS1(330k) 41,175,116 4,529,262,760 585,940 41,175,116 16,426,433 39.89 14,110,491 34.27 74.16
Ave 31,315,883 3,444,747,130 481,194 31,315,883 74.72
Total 751,581,192 82,673,931,120