Kun:LabNotes/MONOD/2015-1-9: Difference between revisions
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*I wrote a script to collect summary statistics for all data sets. | *I wrote a script to collect summary statistics for all data sets. | ||
./[[Media:gather_summary_statistics.txt|gather_summary_statistics.pl]] [[Media:WGBS_UMR_seqCap_sample_file_info.txt|WGBS_UMR_seqCap_sample_file_info.txt]] > WGBS_UMR_seqCap_2014_two_batches_summary_stats.txt | ./[[Media:gather_summary_statistics.txt|gather_summary_statistics.pl]] [[Media:WGBS_UMR_seqCap_sample_file_info.txt|WGBS_UMR_seqCap_sample_file_info.txt]] > WGBS_UMR_seqCap_2014_two_batches_summary_stats.txt | ||
*Two major conclusions: | |||
**Kapa Hyper Prep kit generated libraries of higher complexity and lower clonal rates. | |||
**The NimbleGen capture experiment did on 12/15 was not optimal, which lead to much lower enrichment and on-target capture rate. | |||
*Action item: repeat the capture on the batch of libraries prepared by the Kapa Hyper Prep kit. | |||
{| {{table}} | {| {{table}} | ||
| align="center" style="background:#f0f0f0;"|'''Sample''' | | align="center" style="background:#f0f0f0;"|'''Sample''' |
Latest revision as of 20:27, 14 January 2015
Analysis of the second batch of NimbleGen capture data[edit]
- Noi did the capture experiment: Noi/NOTES/2014-12-25.
- The libraries were sequenced in one HiSeq PE100bp rapid run 141214_SN1001.
- Dinh mapped the reads: Dinh/Dinh_2015/NOTES/2015-1-7.
Quick assessment of the data quality[edit]
- First I checked the performance of target capture.
/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.
Further comparison of the two batches of library preparation and capturing experiments.[edit]
- There were a number of differences on the experimental protocols between the two batches of data.
- 141112_HiSeq: Noi used the Tang et al RRBS method for end-repair and polishing Noi/NOTES/2014-10-29; capture was done on Noi/NOTES/2014-11-4;
- 141216_HiSeq: Noi used the Kapa Hyper Prep kit Noi/NOTES/2014-11-30; capture was done on Noi/NOTES/2014-12-25
- I wrote a script to collect summary statistics for all data sets.
./gather_summary_statistics.pl WGBS_UMR_seqCap_sample_file_info.txt > WGBS_UMR_seqCap_2014_two_batches_summary_stats.txt
- Two major conclusions:
- Kapa Hyper Prep kit generated libraries of higher complexity and lower clonal rates.
- The NimbleGen capture experiment did on 12/15 was not optimal, which lead to much lower enrichment and on-target capture rate.
- Action item: repeat the capture on the batch of libraries prepared by the Kapa Hyper Prep kit.
Sample | Experiment | N_mapped_reads | N_non-clonal_reads | N_on-target_reads | N_non-clonal_on-target_reads | N_on-target_haplotypes | N_target_coverred | Pct_on-target | Pct_clonal |
6-P-1 | 141112_HiSeq | 14,727,691 | 12,016,120 | 6,119,021 | 4,477,865 | 336,894 | 38,344 | 41.5% | 26.82% |
6-P-1 | 141216_HiSeq | 10,355,738 | 10,123,240 | 2,619,216 | 2,523,753 | 233,941 | 36,713 | 25.3% | 3.64% |
6-P-10 | 141112_HiSeq | 12,125,750 | 10,627,443 | 4,622,479 | 3,674,457 | 389,005 | 39,594 | 38.1% | 20.51% |
6-P-2 | 141112_HiSeq | 12,610,235 | 10,592,101 | 4,890,268 | 3,776,213 | 194,655 | 30,935 | 38.8% | 22.78% |
6-P-2 | 141216_HiSeq | 11,570,287 | 11,462,431 | 2,756,445 | 2,724,126 | 882,786 | 44,945 | 23.8% | 1.17% |
6-P-3 | 141112_HiSeq | 13,044,553 | 10,902,745 | 5,089,409 | 3,951,200 | 180,681 | 29,498 | 39.0% | 22.36% |
6-P-3 | 141216_HiSeq | 12,482,525 | 12,258,142 | 4,304,444 | 4,228,174 | 1,154,014 | 45,181 | 34.5% | 1.77% |
6-P-4 | 141112_HiSeq | 11,969,782 | 9,696,006 | 4,662,823 | 3,426,251 | 184,637 | 29,454 | 39.0% | 26.52% |
6-P-8 | 141112_HiSeq | 14,935,803 | 13,198,763 | 6,242,428 | 5,177,911 | 351,452 | 38,772 | 41.8% | 17.05% |
6T-1 | 141216_HiSeq | 11,869,709 | 11,711,949 | 1,631,628 | 1,592,334 | 614,412 | 42,951 | 13.7% | 2.41% |
6T-2 | 141216_HiSeq | 12,820,323 | 12,644,365 | 1,679,917 | 1,605,021 | 535,022 | 42,471 | 13.1% | 4.46% |
6T-3 | 141216_HiSeq | 36,126,640 | 33,993,548 | 6,294,978 | 5,456,336 | 1,390,560 | 45,913 | 17.4% | 13.32% |
6T-4 | 141216_HiSeq | 12,351,984 | 12,219,697 | 1,829,796 | 1,794,578 | 722,787 | 43,545 | 14.8% | 1.92% |
6T-5 | 141216_HiSeq | 13,871,915 | 13,700,144 | 2,047,985 | 2,002,834 | 689,818 | 43,576 | 14.8% | 2.20% |
7-P-10 | 141216_HiSeq | 10,375,497 | 10,108,671 | 2,264,332 | 2,166,347 | 108,343 | 25,759 | 21.8% | 4.33% |
7-P-2 | 141112_HiSeq | 12,071,295 | 10,045,638 | 4,407,555 | 3,544,280 | 86,126 | 17,973 | 36.5% | 19.59% |
7-P-3 | 141216_HiSeq | 8,343,291 | 8,131,342 | 1,913,926 | 1,834,202 | 103,372 | 25,099 | 22.9% | 4.17% |
7-P-5 | 141216_HiSeq | 9,868,792 | 9,790,293 | 2,096,290 | 2,077,736 | 679,672 | 44,364 | 21.2% | 0.89% |
7-P-6 | 141216_HiSeq | 13,420,765 | 13,142,028 | 3,044,464 | 2,934,292 | 235,624 | 36,563 | 22.7% | 3.62% |
7-P-7 | 141216_HiSeq | 13,264,972 | 13,020,148 | 2,601,234 | 2,509,390 | 217,498 | 37,099 | 19.6% | 3.53% |
7-P-8 | 141216_HiSeq | 10,309,480 | 10,046,649 | 2,320,567 | 2,222,588 | 120,025 | 26,514 | 22.5% | 4.22% |
7T-1 | 141216_HiSeq | 12,579,473 | 12,449,866 | 1,685,639 | 1,644,912 | 593,556 | 43,006 | 13.4% | 2.42% |
7T-2 | 141216_HiSeq | 13,386,508 | 13,115,388 | 1,875,500 | 1,768,594 | 402,132 | 40,445 | 14.0% | 5.70% |
7T-4 | 141216_HiSeq | 12,632,367 | 12,486,042 | 1,802,005 | 1,748,412 | 578,586 | 42,950 | 14.3% | 2.97% |
7T-5 | 141216_HiSeq | 13,465,056 | 13,277,929 | 1,888,156 | 1,831,556 | 440,050 | 41,621 | 14.0% | 3.00% |
NC-12 | 141112_HiSeq | 13,489,901 | 11,847,524 | 7,775,540 | 6,528,741 | 668,144 | 43,880 | 57.6% | 16.03% |
NC-13 | 141112_HiSeq | 14,739,045 | 13,565,791 | 8,516,530 | 7,634,190 | 1,026,188 | 45,600 | 57.8% | 10.36% |
NC-14 | 141112_HiSeq | 20,083,892 | 18,545,178 | 12,972,574 | 11,822,645 | 963,541 | 44,221 | 64.6% | 8.86% |
NC-15 | 141112_HiSeq | 14,827,402 | 13,268,019 | 8,506,375 | 7,318,388 | 1,009,294 | 45,460 | 57.4% | 13.97% |
NC-17 | 141112_HiSeq | 13,336,373 | 11,378,302 | 7,670,034 | 6,154,378 | 702,115 | 43,812 | 57.5% | 19.76% |
NC-18 | 141112_HiSeq | 13,248,090 | 11,294,433 | 7,676,163 | 6,176,274 | 513,023 | 42,743 | 57.9% | 19.54% |
NC-2 | 141112_HiSeq | 13,866,539 | 12,827,193 | 7,830,036 | 7,062,215 | 881,306 | 45,316 | 56.5% | 9.81% |
NC-21 | 141112_HiSeq | 16,081,583 | 14,965,703 | 9,245,026 | 8,425,521 | 1,436,801 | 46,192 | 57.5% | 8.86% |
NC-3 | 141112_HiSeq | 16,027,488 | 14,330,418 | 9,380,987 | 8,102,323 | 1,031,698 | 45,529 | 58.5% | 13.63% |
NC-5 | 141112_HiSeq | 11,531,790 | 10,057,121 | 6,516,165 | 5,388,840 | 478,433 | 42,318 | 56.5% | 17.30% |
NC-6 | 141112_HiSeq | 13,434,528 | 12,080,666 | 7,733,596 | 6,691,809 | 867,491 | 45,159 | 57.6% | 13.47% |
NC-7 | 141112_HiSeq | 15,290,119 | 13,970,372 | 8,748,247 | 7,744,173 | 1,137,553 | 45,946 | 57.2% | 11.48% |
NC-7 | 141216_HiSeq | 11,685,910 | 9,211,663 | 4,179,919 | 2,929,376 | 122,228 | 22,142 | 35.8% | 29.92% |
PC-P_2 | 141216_HiSeq | 10,306,946 | 10,206,818 | 2,171,141 | 2,140,765 | 637,877 | 44,379 | 21.1% | 1.40% |
PC-P_4 | 141216_HiSeq | 10,561,291 | 10,419,994 | 2,476,732 | 2,423,078 | 568,230 | 43,728 | 23.5% | 2.17% |
PC-P_9 | 141216_HiSeq | 12,272,000 | 11,995,732 | 3,261,610 | 3,143,222 | 316,171 | 39,834 | 26.6% | 3.63% |
PC-P-3 | 141112_HiSeq | 15,157,128 | 12,617,188 | 7,256,675 | 5,581,424 | 340,207 | 36,891 | 47.9% | 23.09% |
PC-P-4 | 141112_HiSeq | 19,403,398 | 15,071,020 | 10,744,097 | 7,603,427 | 596,193 | 39,582 | 55.4% | 29.23% |
PC-P-5 | 141112_HiSeq | 13,196,672 | 10,533,012 | 5,415,343 | 4,051,510 | 131,556 | 22,886 | 41.0% | 25.18% |
PC-P-6 | 141112_HiSeq | 15,392,120 | 13,176,909 | 6,418,169 | 4,958,048 | 604,369 | 43,138 | 41.7% | 22.75% |
PC-P-7 | 141112_HiSeq | 14,218,885 | 10,784,660 | 5,965,548 | 4,124,202 | 176,841 | 26,171 | 42.0% | 30.87% |
PCT-1 | 141216_HiSeq | 11,921,316 | 11,737,650 | 1,655,540 | 1,607,618 | 389,989 | 41,033 | 13.9% | 2.89% |
PCT-2 | 141216_HiSeq | 14,465,075 | 14,097,386 | 2,031,726 | 1,932,100 | 239,455 | 35,730 | 14.0% | 4.90% |
PCT-4 | 141216_HiSeq | 13,781,204 | 13,569,716 | 1,895,572 | 1,841,279 | 458,181 | 41,897 | 13.8% | 2.86% |
PCT-6 | 141216_HiSeq | 15,681,405 | 15,532,475 | 2,186,241 | 2,149,561 | 882,376 | 44,422 | 13.9% | 1.68% |
PCT-7 | 141216_HiSeq | 12,980,554 | 12,835,501 | 1,973,329 | 1,938,285 | 760,032 | 43,769 | 15.2% | 1.78% |