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 |