Kun:LabNotes/MONOD/2015-3-4
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Analysis of 150209 HiSeq data[edit]
- This is a HiSeq PE200 full run (8-lanes).
- WGBS SeqCap libraries were sequenced in Lane 1-6: AlanFung:LabNotes/2015/2015-1-15.
- WGBS-BSPP libraries were sequenced in Lane 7-8: Noi/NOTES/2014-12-16.
- The yield of this run was low due to over-loading. In addition, Read2 for Lanes 7-8 failed, probably due to some issue with adding the customized sequencing primer.
- Dinh did the read mapping on TSCC and stored the output files in genome-miner.
- Mapping summary. Media:150209_SN216_mapping_summary_statistics.xlsx
- Data folder: /media/Ext12T/DD_Ext12T/MONOD/150209_SN216/
WGBS SeqCap data analysis[edit]
- Both two previous capture experiments have issues.
- WGBS libraries had low complexity due to incomplete end-repair in the first batch of libraries: Kun:LabNotes/MONOD/2014-11-22
- The capture specificity was low for the second batch of libraries, probably because the hyb/wash temperature was off:Kun:LabNotes/MONOD/2015-1-9
- Alan repeated the SeqCap experiments on the good libraries. Even though we obtained less than half of the expected reads due to over-loading, the mapping rates, library complexity and capture specificity is high.
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 | Enrichment_factor |
6P-10 | 150209_SN216 | 11,856,038 | 11,256,409 | 7,605,875 | 7,196,267 | 2,438,845 | 43,116 | 64.2% | 5.1% | 181 |
6P-1 | 150209_SN216 | 15,413,524 | 14,583,601 | 10,144,881 | 9,564,830 | 3,435,116 | 42,275 | 65.8% | 5.4% | 195 |
6P-2 | 150209_SN216 | 22,612,403 | 22,030,892 | 14,895,566 | 14,531,656 | 4,957,911 | 48,888 | 65.9% | 2.6% | 195 |
6P-3 | 150209_SN216 | 28,124,349 | 27,174,711 | 20,126,384 | 19,455,168 | 7,299,019 | 48,605 | 71.6% | 3.4% | 254 |
6P-4 | 150209_SN216 | 17,461,783 | 17,043,271 | 11,210,960 | 10,957,092 | 3,681,845 | 48,765 | 64.2% | 2.4% | 181 |
6P-5 | 150209_SN216 | 18,408,921 | 17,539,470 | 12,021,534 | 11,426,514 | 3,906,601 | 46,620 | 65.3% | 4.7% | 190 |
6P-8 | 150209_SN216 | 15,065,429 | 14,126,133 | 9,848,221 | 9,194,243 | 3,270,856 | 38,575 | 65.4% | 6.2% | 191 |
6P-9 | 150209_SN216 | 15,454,689 | 14,878,257 | 10,106,402 | 9,725,294 | 3,264,835 | 47,884 | 65.4% | 3.7% | 191 |
7P-10 | 150209_SN216 | 16,084,405 | 14,950,041 | 10,304,289 | 9,505,779 | 3,354,725 | 33,688 | 64.1% | 7.1% | 180 |
7P-1 | 150209_SN216 | 17,919,424 | 17,246,658 | 11,811,326 | 11,362,260 | 3,971,753 | 47,927 | 65.9% | 3.8% | 195 |
7P-2 | 150209_SN216 | 18,504,079 | 18,105,418 | 12,338,471 | 12,096,277 | 3,963,752 | 48,496 | 66.7% | 2.2% | 202 |
7P-3 | 150209_SN216 | 17,158,736 | 16,007,892 | 11,097,566 | 10,307,877 | 3,595,366 | 33,801 | 64.7% | 6.7% | 185 |
7P-5 | 150209_SN216 | 16,150,661 | 15,823,154 | 10,781,075 | 10,575,603 | 3,425,413 | 48,578 | 66.8% | 2.0% | 203 |
7P-6 | 150209_SN216 | 17,866,778 | 16,899,877 | 11,705,024 | 11,032,002 | 3,793,696 | 42,107 | 65.5% | 5.4% | 192 |
7P-7 | 150209_SN216 | 12,165,646 | 11,613,860 | 7,657,324 | 7,286,409 | 2,360,706 | 41,902 | 62.9% | 4.5% | 172 |
7P-8 | 150209_SN216 | 17,770,167 | 16,608,765 | 11,568,086 | 10,758,938 | 3,769,299 | 34,189 | 65.1% | 6.5% | 189 |
NC-12 | 150209_SN216 | 12,244,286 | 10,112,656 | 7,326,351 | 5,652,870 | 2,870,082 | 39,640 | 59.8% | 17.4% | 151 |
NC-13 | 150209_SN216 | 13,287,813 | 11,225,562 | 7,401,583 | 5,903,078 | 2,654,620 | 32,461 | 55.7% | 15.5% | 127 |
NC-14 | 150209_SN216 | 15,099,626 | 12,730,307 | 8,558,160 | 6,880,727 | 3,158,255 | 31,238 | 56.7% | 15.7% | 132 |
NC-15 | 150209_SN216 | 10,446,276 | 8,612,619 | 5,886,170 | 4,543,116 | 2,184,901 | 30,527 | 56.3% | 17.6% | 130 |
NC-16 | 150209_SN216 | 16,156,381 | 13,738,488 | 9,240,653 | 7,478,843 | 3,446,998 | 34,619 | 57.2% | 15.0% | 135 |
NC-17 | 150209_SN216 | 11,206,698 | 9,789,484 | 6,148,947 | 5,044,392 | 2,290,114 | 41,055 | 54.9% | 12.6% | 123 |
NC-18 | 150209_SN216 | 17,293,018 | 15,107,659 | 10,390,882 | 8,729,158 | 4,001,526 | 40,831 | 60.1% | 12.6% | 152 |
NC-19 | 150209_SN216 | 9,570,269 | 7,979,380 | 5,301,281 | 4,286,779 | 1,933,377 | 16,690 | 55.4% | 16.6% | 126 |
NC-1 | 150209_SN216 | 8,654,155 | 5,344,362 | 5,429,320 | 2,893,429 | 2,257,693 | 23,221 | 62.7% | 38.2% | 170 |
NC-20 | 150209_SN216 | 11,562,671 | 10,012,200 | 6,384,562 | 5,394,797 | 2,309,928 | 20,759 | 55.2% | 13.4% | 125 |
NC-21 | 150209_SN216 | 9,777,829 | 8,107,699 | 5,309,436 | 4,270,237 | 1,933,542 | 16,770 | 54.3% | 17.1% | 120 |
NC-22 | 150209_SN216 | 10,669,682 | 9,321,773 | 5,988,576 | 4,983,190 | 2,186,536 | 34,616 | 56.1% | 12.6% | 129 |
NC-23 | 150209_SN216 | 9,280,875 | 7,503,208 | 5,110,090 | 3,819,313 | 1,906,292 | 27,111 | 55.1% | 19.2% | 124 |
NC-24 | 150209_SN216 | 10,973,561 | 8,923,809 | 5,863,389 | 4,628,613 | 2,175,281 | 17,511 | 53.4% | 18.7% | 116 |
NC-27 | 150209_SN216 | 10,703,870 | 9,299,108 | 6,189,572 | 5,050,411 | 2,258,083 | 43,697 | 57.8% | 13.1% | 139 |
NC-29 | 150209_SN216 | 8,665,146 | 7,580,097 | 4,695,271 | 3,862,127 | 1,669,828 | 37,120 | 54.2% | 12.5% | 120 |
NC-2 | 150209_SN216 | 12,400,099 | 10,268,646 | 7,753,594 | 6,022,862 | 3,119,326 | 37,584 | 62.5% | 17.2% | 169 |
NC-30 | 150209_SN216 | 15,359,075 | 13,957,906 | 9,350,399 | 8,223,219 | 3,641,546 | 45,664 | 60.9% | 9.1% | 157 |
NC-3 | 150209_SN216 | 14,667,235 | 11,262,855 | 10,229,497 | 7,287,072 | 4,567,306 | 40,214 | 69.7% | 23.2% | 233 |
NC-5 | 150209_SN216 | 10,587,888 | 8,539,647 | 6,081,895 | 4,649,592 | 2,288,865 | 22,576 | 57.4% | 19.3% | 136 |
NC-6 | 150209_SN216 | 17,622,164 | 15,015,455 | 10,094,905 | 8,021,601 | 3,915,231 | 44,816 | 57.3% | 14.8% | 136 |
NC-7 | 150209_SN216 | 11,874,625 | 9,007,398 | 6,915,403 | 4,850,693 | 2,715,436 | 26,210 | 58.2% | 24.1% | 141 |
NC-8 | 150209_SN216 | 10,147,943 | 8,252,437 | 5,625,862 | 4,191,417 | 2,092,717 | 32,803 | 55.4% | 18.7% | 126 |
NC-9 | 150209_SN216 | 13,121,261 | 11,193,953 | 7,632,583 | 6,098,829 | 3,018,621 | 43,001 | 58.2% | 14.7% | 141 |
PCP-2 | 150209_SN216 | 13,694,157 | 13,340,913 | 8,750,769 | 8,535,065 | 2,755,651 | 48,380 | 63.9% | 2.6% | 179 |
PCP-3 | 150209_SN216 | 9,225,527 | 9,067,481 | 6,226,370 | 6,133,490 | 1,984,048 | 47,803 | 67.5% | 1.7% | 210 |
PCP-4 | 150209_SN216 | 17,764,968 | 17,183,802 | 11,699,738 | 11,318,225 | 3,794,030 | 48,009 | 65.9% | 3.3% | 195 |
PCP-5 | 150209_SN216 | 16,764,517 | 16,278,606 | 10,969,639 | 10,661,248 | 3,401,288 | 48,448 | 65.4% | 2.9% | 191 |
PCP-6 | 150209_SN216 | 8,928,969 | 8,767,467 | 6,023,283 | 5,924,473 | 1,944,974 | 47,688 | 67.5% | 1.8% | 210 |
PCP-7 | 150209_SN216 | 19,827,986 | 19,284,552 | 12,908,105 | 12,568,207 | 4,184,040 | 48,723 | 65.1% | 2.7% | 189 |
PCP-8 | 150209_SN216 | 18,503,761 | 17,758,449 | 11,929,727 | 11,437,669 | 3,718,360 | 47,535 | 64.5% | 4.0% | 183 |
PCP-9 | 150209_SN216 | 21,947,480 | 20,712,459 | 14,426,294 | 13,559,086 | 4,835,888 | 44,780 | 65.7% | 5.6% | 194 |
- Direct comparison of read coverage of four samples between the two batches of experiment showed a real improvement. In addition, it appeared that, in at least 3/4 samples, the ends of cfDNA fragments distribute relatively even (no clear hotspot was observed).