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.

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).

File:150209 SN216 seqcap read coverage IGV snapshot.png