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==Analysis of 150209 HiSeq data== *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=== *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. {| {{table}} | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''Experiment''' | align="center" style="background:#f0f0f0;"|'''N_mapped_reads''' | align="center" style="background:#f0f0f0;"|'''N_non-clonal_reads''' | align="center" style="background:#f0f0f0;"|'''N_on-target_reads''' | align="center" style="background:#f0f0f0;"|'''N_non-clonal_on-target_reads''' | align="center" style="background:#f0f0f0;"|'''N_on-target_haplotypes''' | align="center" style="background:#f0f0f0;"|'''N_target_coverred''' | align="center" style="background:#f0f0f0;"|'''Pct_on-target''' | align="center" style="background:#f0f0f0;"|'''Pct_clonal''' | align="center" style="background:#f0f0f0;"|'''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). [[Image:150209_SN216_seqcap_read_coverage_IGV_snapshot.png|1000px]]
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