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===sequencing results=== *statistics and results from combining all the sequencing runs *downampled samples were used in all the following comparison analyses for comparing the IVT method to the Nextera method. *data combined from HL130, HL131, DD04 run *odd that there were more clonal reads in the IVT samples this round, not sure why. but 1000 cell sample worked pretty well. still called many more peaks in IVT samples {| {{table}} | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''sample''' | align="center" style="background:#f0f0f0;"|'''total reads''' | align="center" style="background:#f0f0f0;"|'''one alignment''' | align="center" style="background:#f0f0f0;"|'''one alignment %''' | align="center" style="background:#f0f0f0;"|'''failed to map''' | align="center" style="background:#f0f0f0;"|'''fail map %''' | align="center" style="background:#f0f0f0;"|'''supressed''' | align="center" style="background:#f0f0f0;"|'''supressed %''' | align="center" style="background:#f0f0f0;"|'''clonal reads''' | align="center" style="background:#f0f0f0;"|'''clonal read%''' | align="center" style="background:#f0f0f0;"|'''unique reads''' | align="center" style="background:#f0f0f0;"|'''paired peaks''' | align="center" style="background:#f0f0f0;"|'''peaks''' |- | 1000 cells IVT||s_7_1_Indx49|| 11,921,212 || 8,277,293 ||69.43%|| 2,131,831 ||17.88%|| 1,512,088 ||12.68%|| 308,039 ||3.72%|| 7,969,254 || 654 || 24,848 |- | 500 cells IVT||s_7_1_Indx50|| 12,846,634 || 8,135,684 ||63.33%|| 2,544,528 ||19.81%|| 2,166,422 ||16.86%|| 4,213,575 ||51.79%|| 3,922,109 || 576 || 9,394 |- | 100 cells IVT||s_7_1_Indx51|| 11,696,728 || 4,083,894 ||34.91%|| 2,626,316 ||22.45%|| 4,986,518 ||42.63%|| 2,213,554 ||54.20%|| 1,870,340 || 373 || 1,989 |- | 6 ng purified DNA IVT||s_7_1_Indx52|| 20,394,388 || 13,419,300 ||65.80%|| 3,552,094 ||17.42%|| 3,422,994 ||16.78%|| 6,927,156 ||51.62%|| 6,492,144 || 102 || 3,112 |- | 600 pg purified DNA IVT||s_7_1_Indx53|| 2,761,684 || 343,038 ||12.42%|| 702,766 ||25.45%|| 1,715,880 ||62.13%|| 198,583 ||57.89%|| 144,455 || - || 476 |- | 60 pg purified DNA IVT||s_7_1_Indx54|| 603,428 || 27,006 ||4.48%|| 170,258 ||28.22%|| 406,164 ||67.31%|| 18,584 ||68.81%|| 8,422 || - || 315 |- | 1000 cells Nxtra||s_7_1_Indx55|| 8,585,321 || 5,371,720 ||62.57%|| 1,989,397 ||23.17%|| 1,224,204 ||14.26%|| 2,541,231 ||47.31%|| 2,830,489 || 2,194 || 3,279 |- | 500 cells Nxtra||s_7_1_Indx56|| 28,365,285 || 17,189,378 ||60.60%|| 7,478,535 ||26.37%|| 3,697,372 ||13.03%|| 1,490,960 ||8.67%|| 15,698,418 || 541 || 12,793 |- | 100 cells Nxtra||s_7_1_Indx57|| 42,902,381 || 26,430,162 ||61.61%|| 11,099,059 ||25.87%|| 5,373,160 ||12.52%|| 6,319,086 ||23.91%|| 20,111,076 || 379 || 13,631 |- | 6 ng purified DNA Nxtra||s_7_1_Indx58|| 23,668,232 || 13,653,302 ||57.69%|| 6,268,204 ||26.48%|| 3,746,726 ||15.83%|| 538,700 ||3.95%|| 13,114,602 || 168 || 4,455 |- | 600 pg purified DNA Nxtra||s_7_1_Indx59|| 3,908,464 || 1,831,198 ||46.85%|| 1,343,607 ||34.38%|| 733,659 ||18.77%|| 939,230 ||51.29%|| 891,968 || 34,477 || 7,566 |- | 60 pg purified DNA Nxtra||s_7_1_Indx60|| 1,967,066 || 893,437 ||45.42%|| 790,544 ||40.19%|| 283,085 ||14.39%|| 554,383 ||62.05%|| 339,054 || 8,974 || 988 |- | |} *downsample results *samples 49, 50, 52, 56, 57 58 downsampled to 100 cell IVt total reads amount which was the lowest one in the group above 10 million reads {| {{table}} | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''sample''' | align="center" style="background:#f0f0f0;"|'''total reads''' | align="center" style="background:#f0f0f0;"|'''one alignment''' | align="center" style="background:#f0f0f0;"|'''one alignment %''' | align="center" style="background:#f0f0f0;"|'''failed to map''' | align="center" style="background:#f0f0f0;"|'''fail map %''' | align="center" style="background:#f0f0f0;"|'''supressed''' | align="center" style="background:#f0f0f0;"|'''supressed %''' | align="center" style="background:#f0f0f0;"|'''clonal reads''' | align="center" style="background:#f0f0f0;"|'''clonal read%''' | align="center" style="background:#f0f0f0;"|'''unique reads''' | align="center" style="background:#f0f0f0;"|'''paired peaks''' | align="center" style="background:#f0f0f0;"|'''peaks''' |- | 1000 cells IVT||s_7_1_Indx49|| 11,686,667 || 8,114,449 ||69.43%|| 2,089,796 ||17.88%|| 1,482,422 ||12.68%|| 297,361 ||3.66%|| 7,817,088 || 591 || 24,674 |- | 500 cells IVT||s_7_1_Indx50|| 11,677,578 || 7,395,709 ||63.33%|| 2,312,854 ||19.81%|| 1,969,015 ||16.86%|| 3,505,559 ||47.40%|| 3,890,150 || 543 || 9,583 |- | 100 cells IVT||s_7_1_Indx51|| 11,696,728 || 4,083,894 ||34.91%|| 2,626,316 ||22.45%|| 4,986,518 ||42.63%|| 2,213,554 ||54.20%|| 1,870,340 || 373 || 1,989 |- | 6 ng purified DNA IVT||s_7_1_Indx52|| 11,723,300 || 7,712,924 ||65.79%|| 2,042,896 ||17.43%|| 1,967,480 ||16.78%|| 2,369,254 ||30.72%|| 5,343,670 || 128 || 7,047 |- | 600 pg purified DNA IVT||s_7_1_Indx53|| 2,761,684 || 343,038 ||12.42%|| 702,766 ||25.45%|| 1,715,880 ||62.13%|| 198,583 ||57.89%|| 144,455 || - || 476 |- | 60 pg purified DNA IVT||s_7_1_Indx54|| 603,428 || 27,006 ||4.48%|| 170,258 ||28.22%|| 406,164 ||67.31%|| 18,584 ||68.81%|| 8,422 || - || 315 |- | 1000 cells Nxtra||s_7_1_Indx55|| 8,585,321 || 5,371,720 ||62.57%|| 1,989,397 ||23.17%|| 1,224,204 ||14.26%|| 2,541,231 ||47.31%|| 2,830,489 || 2,194 || 3,279 |- | 500 cells Nxtra||s_7_1_Indx56|| 11,816,738 || 7,161,353 ||60.60%|| 3,116,151 ||26.37%|| 1,539,234 ||13.03%|| 330,186 ||4.61%|| 6,831,167 || 886 || 4,722 |- | 100 cells Nxtra||s_7_1_Indx57|| 11,687,750 || 7,201,722 ||61.62%|| 3,023,309 ||25.87%|| 1,462,719 ||12.51%|| 627,951 ||8.72%|| 6,573,771 || 674 || 4,115 |- | 6 ng purified DNA Nxtra||s_7_1_Indx58|| 11,384,161 || 6,568,137 ||57.70%|| 3,015,484 ||26.49%|| 1,800,540 ||15.82%|| 139,063 ||2.12%|| 6,429,074 || 195 || 2,324 |- | 600 pg purified DNA Nxtra||s_7_1_Indx59|| 3,908,464 || 1,831,198 ||46.85%|| 1,343,607 ||34.38%|| 733,659 ||18.77%|| 939,230 ||51.29%|| 891,968 || 34,477 || 7,566 |- | 60 pg purified DNA Nxtra||s_7_1_Indx60|| 1,967,066 || 893,437 ||45.42%|| 790,544 ||40.19%|| 283,085 ||14.39%|| 554,383 ||62.05%|| 339,054 || 8,974 || 988 |- | |}
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