Kun:LabNotes/MONOD/2015-1-9

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Analysis of the second batch of NimbleGen capture data

 /home/kunzhang/CpgMIP/MONOD/Data/141112_HiSeqRapidRun/get_capture_stats.pl /media/Ext12T/DD_Ext12T/MONOD/141216_HiSeqRapidRun/BAMfiles > 141216_HiSeqRapidRun.capture_stats.txt
Sample total_bases_coverred total_bases on_target_bases_covered on_target_bases Specificity Enrichment_factor
6-P-1 496,391,712 883,938,352 20,732,014 236,943,256 26.81% 37
6-P-2 598,767,372 974,626,668 31,706,660 246,684,036 25.31% 34
6-P-3 543,413,415 1,131,193,408 31,995,541 417,353,349 36.89% 59
6T-1 729,794,959 1,070,341,509 30,151,406 155,220,183 14.50% 17
6T-2 784,299,649 1,158,440,912 29,456,650 159,710,882 13.79% 16
6T-3 1,452,467,042 3,323,804,083 33,406,665 627,923,179 18.89% 24
6T-4 764,174,440 1,132,324,550 30,925,708 176,622,088 15.60% 19
6T-5 843,555,327 1,282,158,923 30,892,326 198,472,950 15.48% 19
7-P-10 465,462,705 897,601,881 10,665,677 208,435,905 23.22% 31
7-P-3 376,857,145 703,513,104 10,510,561 173,576,316 24.67% 33
7-P-5 536,571,852 807,646,898 30,738,662 181,239,774 22.44% 29
7-P-6 616,774,497 1,108,444,523 20,513,185 265,799,682 23.98% 32
7-P-7 658,461,220 1,111,809,575 20,479,249 228,609,307 20.56% 26
7-P-8 439,982,190 839,669,742 11,446,574 201,598,027 24.01% 32
7T-1 780,242,147 1,137,145,477 30,063,836 160,294,067 14.10% 17
7T-2 746,306,547 1,175,101,409 26,503,015 173,809,990 14.79% 18
7T-4 771,225,069 1,142,595,127 29,851,920 171,599,332 15.02% 18
7T-5 802,376,647 1,227,075,648 27,971,718 179,541,336 14.63% 17
NC-7 255,231,717 1,119,499,850 7,739,071 425,057,131 37.97% 62
PC-P_2 563,439,590 865,434,623 30,337,168 193,164,906 22.32% 29
PC-P_4 527,669,028 840,929,316 29,831,801 207,852,537 24.72% 33
PC-P_9 559,749,434 1,035,542,788 24,069,681 289,633,563 27.97% 39
PCT-1 714,410,318 1,064,633,702 27,058,939 155,196,610 14.58% 17
PCT-2 726,354,565 1,275,756,897 19,580,892 189,203,593 14.83% 18
PCT-4 815,323,371 1,247,319,961 28,462,046 179,280,115 14.37% 17
PCT-6 948,428,968 1,450,561,748 31,894,490 214,220,998 14.77% 18
PCT-7 796,647,247 1,191,900,342 31,314,595 191,113,213 16.03% 19
  • Here is the results for the first capture experiment (141112_SN1001).
Sample total_bases_coverred total_bases on_target_bases_covered on_target_bases Specificity Enrichment_factor
SeqCap-pCancerSetA-Nov4_12 138,931,528 1,168,877,279 5,883,919 450,558,243 38.5% 63
SeqCap-pCancerSetA-Nov4_13 369,134,874 1,424,314,151 21,209,194 614,835,055 43.2% 77
SeqCap-pCancerSetA-Nov4_14 302,700,391 1,203,488,680 13,952,014 489,036,528 40.6% 69
SeqCap-pCancerSetA-Nov4_15 277,562,818 1,250,329,814 12,577,032 511,943,961 40.9% 70
SeqCap-pCancerSetA-Nov4_16 274,256,170 1,164,394,023 12,418,863 474,550,198 40.8% 70
SeqCap-pCancerSetA-Nov4_18 403,128,602 1,170,296,929 23,073,184 461,126,140 39.4% 66
SeqCap-pCancerSetA-Nov4_19 385,167,143 1,417,434,873 22,614,122 614,480,251 43.4% 77
SeqCap-pCancerSetA-Nov4_2 354,784,810 1,514,708,612 19,490,111 751,025,646 49.6% 99
SeqCap-pCancerSetA-Nov4_4 352,108,468 2,000,885,721 23,609,719 1,141,652,594 57.1% 134
SeqCap-pCancerSetA-Nov4_5 196,108,966 1,300,234,129 8,246,274 563,004,318 43.3% 77
SeqCap-pCancerSetA-Nov4_6 450,502,450 1,502,032,451 28,135,196 645,300,745 43.0% 76
SeqCap-pCancerSetA-Nov4_7 226,755,475 1,432,933,860 10,016,683 629,536,922 43.9% 79
SeqCap-pNormalSetA-Nov4_12 368,272,742 1,450,833,379 32,791,421 853,947,465 58.9% 145
SeqCap-pNormalSetA-Nov4_13 330,611,335 1,291,478,405 29,764,564 756,289,960 58.6% 143
SeqCap-pNormalSetA-Nov4_14 360,000,998 1,364,998,815 32,082,346 801,469,734 58.7% 144
SeqCap-pNormalSetA-Nov4_15 375,193,438 1,970,841,697 30,241,737 1,295,408,500 65.7% 194
SeqCap-pNormalSetA-Nov4_16 365,138,307 1,417,821,628 31,787,247 825,520,233 58.2% 141
SeqCap-pNormalSetA-Nov4_18 326,952,891 1,305,603,890 28,937,598 760,701,025 58.3% 141
SeqCap-pNormalSetA-Nov4_19 312,924,926 1,271,134,775 27,505,559 749,645,411 59.0% 145
SeqCap-pNormalSetA-Nov4_2 353,552,883 1,275,196,941 31,331,422 731,603,678 57.4% 136
SeqCap-pNormalSetA-Nov4_4 354,621,865 1,456,339,179 31,829,571 867,560,025 59.6% 149
SeqCap-pNormalSetA-Nov4_5 291,891,632 1,066,253,299 27,061,797 618,610,388 58.0% 140
SeqCap-pNormalSetA-Nov4_6 333,830,242 1,234,362,498 31,357,436 723,278,371 58.6% 143
SeqCap-pNormalSetA-Nov4_7 377,475,888 1,451,628,039 32,325,421 843,343,133 58.1% 140
  • For some reason the specificity and enrichment factors for the second experiment is much worse than the first one.