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==Probe Bias== * Calculate probe bias to re-subset probes as in Deng 2009 NBT paper. * Also, identify issues with the zero or low coverage mandatory and recommended sites and re-design probes. ===Identify problematic probes for mandatory and recommended targets=== * Note: recommended_29 and recommended_30 became optional. * Note: found wrong position given for mandatory_1 and mandatory_15 in the excel table, fix the positions in my reference table. * All of the sites with low or 0 probe efficiency were not covered. Thus, the missed sites were due to only inefficiency of the probes on either or both strands. * '''Missing both strands for:''' mandatory_11 (no coverage) mandatory_16 (no coverage) recommended_4 (unable to design probe for before) recommended_21 (no coverage) recommended_20 (low efficiency) recommended_27 (low efficiency) * '''Watson only''' recommended_2 recommended_5 recommended_8 recommended_22 recommended_25 mandatory_15 mandatory_2 (low efficiency) mandatory_8 (low efficiency) mandatory_10 (low efficiency) mandatory_14 (low efficiency) recommended_9 (low efficiency) recommended_23 (low efficiency) * '''Crick only''' mandatory_5 recommended_16 mandatory_4 (low efficiency) <nowiki> reads site str 23892 mandatory_13:chr15:100249085-100249289 + 12876 mandatory_10:chr7:3025508-3025737 - 5540 mandatory_3:chr4:7526550-7526760 - 4183 mandatory_15:chr17:75369137-75369338 - 3944 mandatory_1:chr4:154710370-154710640 + 2965 mandatory_8:chr7:140218006-140218261 - 2579 mandatory_5:chr2:9518172-9518402 + 1839 mandatory_6:chr17:80709116-80709327 - 1358 mandatory_9:chr7:26206450-26206690 - 805 mandatory_14:chr4:147557728-147557999 - 633 mandatory_9:chr7:26206446-26206652 + 561 mandatory_12:chr2:42275654-42275925 + 537 mandatory_7:chr3:142837896-142838117 - 484 mandatory_7:chr3:142837897-142838117 + 331 mandatory_12:chr2:42275614-42275844 - 231 mandatory_13:chr15:100249082-100249302 - 230 mandatory_3:chr4:7526557-7526773 + 183 mandatory_6:chr17:80709042-80709272 + 67 mandatory_2:chr1:110052333-110052595 - 32 mandatory_4:chr2:164593111-164593326 + 17 mandatory_4:chr2:164593173-164593378 - 16 mandatory_14:chr4:147557730-147558008 + 9 mandatory_8:chr7:140218000-140218270 + 5 mandatory_2:chr1:110052282-110052542 + 5 mandatory_1:chr4:154710373-154710633 - 5 mandatory_10:chr7:3025518-3025736 + 0 mandatory_15:chr17:75369134-75369334 + 0 mandatory_5:chr2:9518220-9518443 - 0 mandatory_11:chr7:138229771-138230020 + 0 mandatory_11:chr7:138229843-138230113 - 0 mandatory_16:chr7:93520143-93520413 - </nowiki> ===Recommended=== <nowiki> reads site str 65845 recommended_33:chr8:3316771-3316991 + 19194 recommended_34:chr1:25257453-25257723 - 12188 recommended_14:chr17:43339401-43339611 - 12048 recommended_11:chr21:47783987-47784263 + 11668 recommended_24:chr1:115124392-115124598 - 11231 recommended_31:chrX:135333528-135333788 - 11132 recommended_5:chr7:27154944-27155156 - 10747 recommended_19:chr16:1017670-1017944 - 9879 recommended_6:chr10:7451206-7451436 - 7055 recommended_32:chr17:1633600-1633820 - 6674 recommended_10:chr1:161442627-161442877 + 5537 recommended_28:chr17:43044892-43045132 + 4945 recommended_15:chr16:85676275-85676545 + 4350 recommended_23:chr6:32042899-32043159 - 4311 recommended_3:chr19:38085548-38085818 - 2204 recommended_9:chr13:103052745-103053015 - 2117 recommended_13:chr20:36013306-36013546 + 2010 recommended_32:chr17:1633600-1633820 + 1950 recommended_22:chr7:71682175-71682435 - 1822 recommended_1:chr5:54281139-54281408 - 1516 recommended_19:chr16:1017669-1017943 + 1285 recommended_7:chr17:7165161-7165397 - 1185 recommended_13:chr20:36013306-36013536 - 1163 recommended_18:chr11:69197082-69197351 - 981 recommended_11:chr21:47783999-47784254 - 934 recommended_33:chr8:3316763-3316986 - 900 recommended_26:chr1:3567532-3567752 - 773 recommended_28:chr17:43044890-43045150 - 720 recommended_17:chr17:76921742-76921982 + 714 recommended_26:chr1:3567513-3567773 + 676 recommended_10:chr1:161442625-161442877 - 627 recommended_25:chr12:130589110-130589320 - 504 recommended_24:chr1:115124345-115124605 + 448 recommended_18:chr11:69197079-69197355 + 410 recommended_7:chr17:7165139-7165351 + 354 recommended_3:chr19:38085549-38085819 + 297 recommended_2:chr20:20349143-20349401 - 241 recommended_24:chr1:115124345-115124605 - 206 recommended_17:chr17:76921738-76921961 - 123 recommended_15:chr16:85676279-85676544 - 119 recommended_12:chr2:8597284-8597533 + 94 recommended_6:chr10:7451190-7451465 + 91 recommended_8:chr2:9614480-9614708 - 88 recommended_1:chr5:54281139-54281409 + 58 recommended_34:chr1:25257451-25257727 + 53 recommended_31:chrX:135333568-135333778 + 43 recommended_16:chr4:118975389-118975609 + 39 recommended_12:chr2:8597159-8597438 - 16 recommended_27:chr16:1243456-1243666 + 8 recommended_9:chr13:103052712-103052935 + 7 recommended_20:chr8:74878400-74878650 - 4 recommended_27:chr16:1243426-1243663 - 2 recommended_23:chr6:32042893-32043163 + 0 recommended_21:chr10:125853024-125853277 - 0 recommended_25:chr12:130588995-130589226 + 0 recommended_32:chr17:1633599-1633825 + 0 recommended_14:chr17:43339405-43339665 + 0 recommended_2:chr20:20349125-20349399 + 0 recommended_8:chr2:9614470-9614722 + 0 recommended_16:chr4:118975389-118975619 - 0 recommended_5:chr7:27154941-27155143 + 0 recommended_22:chr7:71682176-71682426 + 0 recommended_20:chr8:74878348-74878592 + </nowiki> {| {{table}} border=1 | align="center" style="background:#f0f0f0;"|'''order''' | align="center" style="background:#f0f0f0;"|'''locus_identifier''' | align="center" style="background:#f0f0f0;"|'''chrom''' | align="center" style="background:#f0f0f0;"|'''probe_id''' | align="center" style="background:#f0f0f0;"|'''probe_strand''' | align="center" style="background:#f0f0f0;"|'''Crick total''' | align="center" style="background:#f0f0f0;"|'''Watson total''' | align="center" style="background:#f0f0f0;"|'''Capture''' |- | 3||mandatory_3||chr4||cg14372037||+||1711||83||Both |- | 6||mandatory_6||chr17||cg00960700||-||476||46||Both |- | 7||mandatory_7||chr3||cg19442495||+||290||122||Both |- | 9||mandatory_9||chr7||cg07945582||+||1346||486||Both |- | 12||mandatory_12||chr2||cg12630082||+||107||242||Both |- | 13||mandatory_13||chr15||cg07382129||+||194||4162||Both |- | 17||recommended_1||chr5||cg06837426||-||584||43||Both |- | 19||recommended_3||chr19||cg27321876||-||1345||102||Both |- | 22||recommended_6||chr10||cg09060610||-||3789||61||Both |- | 23||recommended_7||chr17||cg15298719||-||2017||77||Both |- | 26||recommended_10||chr1||cg09846895||-||303||2362||Both |- | 27||recommended_11||chr21||cg05931989||-||400||2966||Both |- | 28||recommended_12||chr2||cg09590377||-||16||39||Both |- | 29||recommended_13||chr20||cg23635789||+||448||1050||Both |- | 30||recommended_14||chr17||cg03048083||-||4300||222||Both |- | 31||recommended_15||chr16||cg26648465||-||387||1073||Both |- | 33||recommended_17||chr17||cg05306745||+||69||337||Both |- | 34||recommended_18||chr11||cg25169679||-||560||535||Both |- | 35||recommended_19||chr16||cg07197480||-||4091||494||Both |- | 40||recommended_24||chr1||cg20145149||-||4970||417||Both |- | 42||recommended_26||chr1||cg07382920||-||320||500||Both |- | 44||recommended_28||chr17||cg04819499||-||569||2377||Both |- | 47||recommended_31||chrX||cg24347720||+||5337||378||Both |- | 48||recommended_32||chr17||cg21824343||+||2088||593||Both |- | 49||recommended_33||chr8||cg00552087||-||263||15227||Both |- | 50||recommended_34||chr1||cg24019564||-||11625||489||Both |- | 5||mandatory_5||chr2||cg19426625||-||0||1695||Watson only |- | 32||recommended_16||chr4||cg12311175||+||0||45||Watson only |- | 36||recommended_20||chr8||cg17316966||+||8||0||Low both |- | 43||recommended_27||chr16||cg01128460||-||1||9||Low both |- | 2||mandatory_2||chr1||cg21646186||+||51||8||Low Watson |- | 8||mandatory_8||chr7||cg06310157||-||1719||11||Low Watson |- | 10||mandatory_10||chr7||cg15025536||+||3067||1||Low Watson |- | 14||mandatory_14||chr4||cg01572513||-||509||11||Low Watson |- | 25||recommended_9||chr13||cg22583065||+||913||6||Low Watson |- | 39||recommended_23||chr6||cg14173662||-||1651||3||Low Watson |- | 4||mandatory_4||chr2||cg04457196||+||3||30||Low Crick |- | 1||mandatory_1||chr4||cg22178613||-||185||7486||Both |- | 11||mandatory_11||chr7||cg12743416||-||0||0||None |- | 15||mandatory_15||chr17||cg15044248||+||2676||0||Crick only |- | 16||mandatory_16||chr7||cg24084681||+||0||0||None |- | 20||recommended_4||chr16||cg06405517||-||0||0||None |- | 37||recommended_21||chr10||cg00660608||-||0||0||None |- | 45||recommended_29||chr4||cg22475974||+||0||0||None |- | 46||recommended_30||chr7||cg18278817||-||0||0||None |- | 18||recommended_2||chr20||cg00648301||+||134||0||Crick only |- | 21||recommended_5||chr7||cg18680977||-||4863||0||Crick only |- | 24||recommended_8||chr2||cg05986044||+||63||0||Crick only |- | 38||recommended_22||chr7||cg09361748||-||698||0||Crick only |- | 41||recommended_25||chr12||cg21898944||-||335||0||Crick only |}
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