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= Data analysis of sequencing library of Parkinson's patient samples from Burnham Institute= * Sequencing library ID: '''NP-220K-Parkinson_Ind1-18-Feb15, HL089 run''' * Library construction: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-2-15]] == Sample information == {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Pair''' | align="center" style="background:#f0f0f0;"|'''Control Sample ID''' | align="center" style="background:#f0f0f0;"|'''Sample code''' | align="center" style="background:#f0f0f0;"|'''Sex''' | align="center" style="background:#f0f0f0;"|'''age (year.day)''' | align="center" style="background:#f0f0f0;"|'''Postmortem time''' | align="center" style="background:#f0f0f0;"|'''PD Sample ID''' | align="center" style="background:#f0f0f0;"|'''Sample code''' | align="center" style="background:#f0f0f0;"|'''Sex''' | align="center" style="background:#f0f0f0;"|'''age (year.day)''' | align="center" style="background:#f0f0f0;"|'''Postmortem time''' |- | 1||5028||P1C||M||67.293||P18||1947||P1P||M||70.251||P17 |- | 2||4789||P2C||F||72.053||P19||4977||P2P||F||76.081||P14 |- | 3||5171||P3C||M||79.088||P05||4879||P3P||M||75.351||P15 |- | 4||1818||P4C||M||76.294||P03||4526||P4P||M||78.182||P01 |- | 5||5089||P5C||M||89.018||P14||5203||P5P||M||89.06||P10 |- | 6||5237||P6C||M||52.291||P13||1910||P6P||M||51.243||P10 |- | 7||1569||P7C1||F||77.089||P08||1401||P7P||F||80.215||P04 |- | 7||5219||P7C2||F||76.348||P03|||||||||| |- | 8||4735||P8C||M||73.184||P21||1741||P8P1||M||71.348||P20 |- | 8||||||||||||5306||P8P2||M||76.311||P21 |}<br> = DMR220k mapping by SOAP (before trimming) = {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''Fastq file''' | align="center" style="background:#f0f0f0;"|'''#Mappable reads''' | align="center" style="background:#f0f0f0;"|'''#Mapped reads''' | align="center" style="background:#f0f0f0;"|'''Mapping Rate''' | align="center" style="background:#f0f0f0;"|'''Combined Mapping Rate''' |- | P1C||P1C_1.txt.fwd.soap.PE.out||11587217||4532458||39.12(%)||75.28% |- | ||P1C_1.txt.rev.soap.PE.out||11587217||4189445||36.16(%)|| |- | P2C||P2C_1.txt.fwd.soap.PE.out||15881433||6006681||37.82(%)||71.97% |- | ||P2C_1.txt.rev.soap.PE.out||15881433||5422813||34.15(%)|| |- | P3C||P3C_1.txt.fwd.soap.PE.out||11143726||4292874||38.52(%)||74.06% |- | ||P3C_1.txt.rev.soap.PE.out||11143726||3960855||35.54(%)|| |- | P4C||P4C_1.txt.fwd.soap.PE.out||12849788||4630353||36.03(%)||69.19% |- | ||P4C_1.txt.rev.soap.PE.out||12849788||4261621||33.16(%)|| |- | P5C||P5C_1.txt.fwd.soap.PE.out||14221122||5724586||40.25(%)||77.03% |- | ||P5C_1.txt.rev.soap.PE.out||14221122||5230402||36.78(%)|| |- | P6C||P6C_1.txt.fwd.soap.PE.out||14112863||5168312||36.62(%)||70.35% |- | ||P6C_1.txt.rev.soap.PE.out||14112863||4760129||33.73(%)|| |- | P7C1||P7C1_1.txt.fwd.soap.PE.out||13273426||5029339||37.89(%)||72.48% |- | ||P7C1_1.txt.rev.soap.PE.out||13273426||4590775||34.59(%)|| |- | P7C2||P7C2_1.txt.fwd.soap.PE.out||10804019||4102770||37.97(%)||73.93% |- | ||P7C2_1.txt.rev.soap.PE.out||10804019||3884944||35.96(%)|| |- | P8C||P8C_1.txt.fwd.soap.PE.out||11113577||3978002||35.79(%)||68.72% |- | ||P8C_1.txt.rev.soap.PE.out||11113577||3660086||32.93(%)|| |- | P1P||P1P_1.txt.fwd.soap.PE.out||11887236||4435830||37.32(%)||71.40% |- | ||P1P_1.txt.rev.soap.PE.out||11887236||4051377||34.08(%)|| |- | P2P||P2P_1.txt.fwd.soap.PE.out||10570835||3719618||35.19(%)||67.49% |- | ||P2P_1.txt.rev.soap.PE.out||10570835||3414342||32.30(%)|| |- | P3P||P3P_1.txt.fwd.soap.PE.out||12343982||4467880||36.19(%)||69.43% |- | ||P3P_1.txt.rev.soap.PE.out||12343982||4103164||33.24(%)|| |- | P4P||P4P_1.txt.fwd.soap.PE.out||13306437||4612404||34.66(%)||66.16% |- | ||P4P_1.txt.rev.soap.PE.out||13306437||4191194||31.50(%)|| |- | P5P||P5P_1.txt.fwd.soap.PE.out||16356159||6335050||38.73(%)||75.05% |- | ||P5P_1.txt.rev.soap.PE.out||16356159||5941194||36.32(%)|| |- | P6P||P6P_1.txt.fwd.soap.PE.out||12406211||4691026||37.81(%)||72.84% |- | ||P6P_1.txt.rev.soap.PE.out||12406211||4345710||35.03(%)|| |- | P7P||P7P_1.txt.fwd.soap.PE.out||14361383||5263978||36.65(%)||71.46% |- | ||P7P_1.txt.rev.soap.PE.out||14361383||4998621||34.81(%)|| |- | P8P1||P8P1_1.txt.fwd.soap.PE.out||15686569||6074276||38.72(%)||74.48% |- | ||P8P1_1.txt.rev.soap.PE.out||15686569||5608916||35.76(%)|| |- | P8P2||P8P2_1.txt.fwd.soap.PE.out||13317181||4960421||37.25(%)||72.68% |- | ||P8P2_1.txt.rev.soap.PE.out||13317181||4718163||35.43(%)|| |}<br> = DMR220k mapping by SOAP (after trimming) = * Dr. Zhang had the comment that the MmeI digestion in N2-adpator protocol only digested 18/20bp off the capturing arms and leaves another 8-10bp of sequences. He found that trimming the 8-10bp sequences from the 5'-ends of the sequencing reads improved the accuracy of the assay. The methylation levels measured from the two DNA strands (the Watson strand and the Crick strand) of the same CpG sites were compared and the correlate coefficient were calculated. (He suggested to see Supp Figure 2a in his 2009 NBT paper)<br><br> {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''Fastq file''' | align="center" style="background:#f0f0f0;"|'''#Mappable reads''' | align="center" style="background:#f0f0f0;"|'''#Mapped reads''' | align="center" style="background:#f0f0f0;"|'''Mapping Rate''' | align="center" style="background:#f0f0f0;"|'''Combined Mapping Rate''' |- | P1C||P1C_1.txt.trimmed.fwd.soap.PE.out||11587217||4651950||40.15(%)||77.26% |- | ||P1C_1.txt.trimmed.rev.soap.PE.out||11587217||4300295||37.11(%)|| |- | P2C||P2C_1.txt.trimmed.fwd.soap.PE.out||15881433||6153226||38.74(%)||73.76% |- | ||P2C_1.txt.trimmed.rev.soap.PE.out||15881433||5562135||35.02(%)|| |- | P3C||P3C_1.txt.trimmed.fwd.soap.PE.out||11143726||4394150||39.43(%)||75.85% |- | ||P3C_1.txt.trimmed.rev.soap.PE.out||11143726||4058568||36.42(%)|| |- | P4C||P4C_1.txt.trimmed.fwd.soap.PE.out||12849788||4755798||37.01(%)||71.09% |- | ||P4C_1.txt.trimmed.rev.soap.PE.out||12849788||4379149||34.08(%)|| |- | P5C||P5C_1.txt.trimmed.fwd.soap.PE.out||14221122||5870051||41.28(%)||79.00% |- | ||P5C_1.txt.trimmed.rev.soap.PE.out||14221122||5363985||37.72(%)|| |- | P6C||P6C_1.txt.trimmed.fwd.soap.PE.out||14112863||5300550||37.56(%)||72.17% |- | ||P6C_1.txt.trimmed.rev.soap.PE.out||14112863||4884889||34.61(%)|| |- | P7C1||P7C1_1.txt.trimmed.fwd.soap.PE.out||13273426||5153728||38.83(%)||74.30% |- | ||P7C1_1.txt.trimmed.rev.soap.PE.out||13273426||4708161||35.47(%)|| |- | P7C2||P7C2_1.txt.trimmed.fwd.soap.PE.out||10804019||4203376||38.91(%)||75.75% |- | ||P7C2_1.txt.trimmed.rev.soap.PE.out||10804019||3980496||36.84(%)|| |- | P8C||P8C_1.txt.trimmed.fwd.soap.PE.out||11113577||4087969||36.78(%)||70.64% |- | ||P8C_1.txt.trimmed.rev.soap.PE.out||11113577||3763353||33.86(%)|| |- | P1P||P1P_1.txt.trimmed.fwd.soap.PE.out||11887236||4553543||38.31(%)||73.35% |- | ||P1P_1.txt.trimmed.rev.soap.PE.out||11887236||4165062||35.04(%)|| |- | P2P||P2P_1.txt.trimmed.fwd.soap.PE.out||10570835||3823742||36.17(%)||69.41% |- | ||P2P_1.txt.trimmed.rev.soap.PE.out||10570835||3513607||33.24(%)|| |- | P3P||P3P_1.txt.trimmed.fwd.soap.PE.out||12343982||4596931||37.24(%)||71.48% |- | ||P3P_1.txt.trimmed.rev.soap.PE.out||12343982||4226905||34.24(%)|| |- | P4P||P4P_1.txt.trimmed.fwd.soap.PE.out||13306437||4737667||35.60(%)||67.98% |- | ||P4P_1.txt.trimmed.rev.soap.PE.out||13306437||4308188||32.38(%)|| |- | P5P||P5P_1.txt.trimmed.fwd.soap.PE.out||16356159||6501010||39.75(%)||77.01% |- | ||P5P_1.txt.trimmed.rev.soap.PE.out||16356159||6094805||37.26(%)|| |- | P6P||P6P_1.txt.trimmed.fwd.soap.PE.out||12406211||4811998||38.79(%)||74.75% |- | ||P6P_1.txt.trimmed.rev.soap.PE.out||12406211||4460799||35.96(%)|| |- | P7P||P7P_1.txt.trimmed.fwd.soap.PE.out||14361383||5407295||37.65(%)||73.39% |- | ||P7P_1.txt.trimmed.rev.soap.PE.out||14361383||5132459||35.74(%)|| |- | P8P1||P8P1_1.txt.trimmed.fwd.soap.PE.out||15686569||6216980||39.63(%)||76.25% |- | ||P8P1_1.txt.trimmed.rev.soap.PE.out||15686569||5744721||36.62(%)|| |- | P8P2||P8P2_1.txt.trimmed.fwd.soap.PE.out||13317181||5099724||38.29(%)||74.65% |- | ||P8P2_1.txt.trimmed.rev.soap.PE.out||13317181||4841963||36.36(%)|| |}<br> {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''Correlation coefficient<br>MinDepth=10''' | align="center" style="background:#f0f0f0;"|'''Correlation coefficient<br>MinDepth=50''' | align="center" style="background:#f0f0f0;"|'''#of cycles''' | align="center" style="background:#f0f0f0;"|'''Ct value''' | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''Correlation coefficient<br>MinDepth=10''' | align="center" style="background:#f0f0f0;"|'''Correlation coefficient<br>MinDepth=50''' |- | P1P(trimmed)||0.961||||13||11.46||P1P||0.935||0.957 |- | P4P(trimmed)||0.960||||13||11.4||P4P||0.934||0.956 |- | P1C (trimmed)||0.957||0.980||13||10.84||P1C||0.925||0.953 |- | P2P(trimmed)||0.951||||13||11.45||P2P||0.924||0.951 |- | P4C(trimmed)||0.947|| ||13||11.25||P4C||0.918||0.947 |- | P3P(trimmed)||0.946||||13||11.2||P3P||0.917||0.952 |- | P8C(trimmed)||0.941||||14||12.38||P8C||0.912||0.949 |- | P2C(trimmed)||0.936||||16||13.15||P2C||0.913||0.947 |- | P3C(trimmed)||0.934||||16||13.49||P3C||0.909||0.947 |- | P5C(trimmed)||0.927||||16||13.81||P5C||0.900||0.939 |- | P8P1(trimmed)||0.917||||17||14.36|||||| |- | P6P(trimmed)||0.912||||17||14.52||P6P||0.885||0.927 |- | P8P2(trimmed)||0.912||||17||14.46|||||| |- | P5P(trimmed)||0.900||||17||14.91||P5P||0.873||0.923 |- | P6C(trimmed)||0.889||||17||14.83||P6C||0.860||0.912 |- | P7C1(trimmed)||0.866||0.917||17||14.75 |- | P7P(trimmed)||0.828||0.896||20||16.42 |- | P7C2(trimmed)||0.789||0.882||20||17.73 |}<br> [[File:capturing eff effect-2.png| 700px]]<br> == Histogram plot == [[File:histogram001.png]] [[File:histogram002.png]] [[File:histogram003.png]] [[File:histogram004.png]] == DMS rate == {| {{table}}border = 1 | align="center" style="background:#f0f0f0;"|'''Samples''' | align="center" style="background:#f0f0f0;"|'''DMS rate''' |- | Pair1||3.40% |- | Pair2||0.78% |- | Pair3||2.20% |- | Pair4||7.30% |- | Pair5||8.30% |- | Pair8-1||3.74% |- | Pair8-2||2.17% |}<br> [[File:hcorcluster.PNG]] * Discussion with Dr. Zhang (2011_03_25) details later...... * Rate of mapping after merging trimmed reads and use SE mapping {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''Fastq file''' | align="center" style="background:#f0f0f0;"|'''#Mappable reads''' | align="center" style="background:#f0f0f0;"|'''#Mapped reads''' | align="center" style="background:#f0f0f0;"|'''Mapping Rate''' | align="center" style="background:#f0f0f0;"|'''Combined Mapping Rate''' |- | P1C||P1C_merge_trimmed.txt.fwd.soap.out||23174434||10372464||44.76||86.24 |- | ||P1C_merge_trimmed.txt.rev.soap.out||23174434||9613416||41.48|| |- | P2C||P2C_merge_trimmed.txt.fwd.soap.out||31762866||14121330||44.46||84.96 |- | ||P2C_merge_trimmed.txt.rev.soap.out||31762866||12864985||40.5|| |- | P3C||P3C_merge_trimmed.txt.fwd.soap.out||22287452||9936569||44.58||86.02 |- | ||P3C_merge_trimmed.txt.rev.soap.out||22287452||9234947||41.44|| |- | P4C||P4C_merge_trimmed.txt.fwd.soap.out||25699576||11034635||42.94||82.76 |- | ||P4C_merge_trimmed.txt.rev.soap.out||25699576||10233236||39.82|| |- | P5C||P5C_merge_trimmed.txt.fwd.soap.out||28442244||13010973||45.75||87.79 |- | ||P5C_merge_trimmed.txt.rev.soap.out||28442244||11956478||42.04|| |- | P8C||P8C_merge_trimmed.txt.fwd.soap.out||22227154||9521201||42.84||82.59 |- | ||P8C_merge_trimmed.txt.rev.soap.out||22227154||8836127||39.75|| |- | P1P||P1P_merge_trimmed.txt.fwd.soap.out||23774472||10393409||43.72||83.94 |- | ||P1P_merge_trimmed.txt.rev.soap.out||23774472||9561766||40.22|| |- | P2P||P2P_merge_trimmed.txt.fwd.soap.out||21141670||8980185||42.48||81.82 |- | ||P2P_merge_trimmed.txt.rev.soap.out||21141670||8317535||39.34|| |- | P3P||P3P_merge_trimmed.txt.fwd.soap.out||24687964||10578294||42.85||82.44 |- | ||P3P_merge_trimmed.txt.rev.soap.out||24687964||9772971||39.59|| |- | P4P||P4P_merge_trimmed.txt.fwd.soap.out||26612874||11243003||42.25||80.96 |- | ||P4P_merge_trimmed.txt.rev.soap.out||26612874||10302628||38.71|| |- | P5P||P5P_merge_trimmed.txt.fwd.soap.out||32712318||14537861||44.44||86.29 |- | ||P5P_merge_trimmed.txt.rev.soap.out||32712318||13691284||41.85|| |- | P8P1||P8P1_merge_trimmed.txt.fwd.soap.out||31373138||13957523||44.49||85.82 |- | ||P8P1_merge_trimmed.txt.rev.soap.out||31373138||12967094||41.33|| |- | P8P2||P8P2_merge_trimmed.txt.fwd.soap.out||26634362||11565590||43.42||85.32 |- | ||P8P2_merge_trimmed.txt.rev.soap.out||26634362||11160054||41.9|| |}<br> * Correlation coefficient is pretty much the same {| {{table}} border =1 | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''N''' | align="center" style="background:#f0f0f0;"|'''MinDepth=10''' |- | P1P||41598||0.961 |- | P4P||49478||0.960 |- | P1C||47853||0.954 |- | P2P||41806||0.951 |- | P4C||49746||0.947 |- | P3P||46043||0.946 |- | P8C||40076||0.941 |- | P2C||42901||0.935 |- | P3C||38510||0.934 |- | P5C||48785||0.927 |- | P8P1||44087||0.917 |- | P8P2||46714||0.911 |- | P5P||55131||0.900 |}<br>
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