Noi/NOTES/2011-3-17: Difference between revisions
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| 8||||||||||||5306||P8P2||M||76.311||P21 | | 8||||||||||||5306||P8P2||M||76.311||P21 | ||
|}<br> | |}<br> | ||
= DMR220k mapping by SOAP = | = DMR220k mapping by SOAP (before trimming) = | ||
{| {{table}} border = 1 | {| {{table}} border = 1 | ||
| align="center" style="background:#f0f0f0;"|'''Sample''' | | align="center" style="background:#f0f0f0;"|'''Sample''' | ||
Line 45: | Line 45: | ||
| align="center" style="background:#f0f0f0;"|'''Combined 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||P1C_1.txt.fwd.soap.PE.out||11587217||4532458||39.12(%)||75.28% | ||
|- | |- | ||
| ||P1C_1.txt.rev.soap.PE.out||11587217||4189445||36.16|| | | ||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||P2C_1.txt.fwd.soap.PE.out||15881433||6006681||37.82(%)||71.97% | ||
|- | |- | ||
| ||P2C_1.txt.rev.soap.PE.out||15881433||5422813||34.15|| | | ||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||P3C_1.txt.fwd.soap.PE.out||11143726||4292874||38.52(%)||74.06% | ||
|- | |- | ||
| ||P3C_1.txt.rev.soap.PE.out||11143726||3960855||35.54|| | | ||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||P4C_1.txt.fwd.soap.PE.out||12849788||4630353||36.03(%)||69.19% | ||
|- | |- | ||
| ||P4C_1.txt.rev.soap.PE.out||12849788||4261621||33.16|| | | ||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||P5C_1.txt.fwd.soap.PE.out||14221122||5724586||40.25(%)||77.03% | ||
|- | |- | ||
| ||P5C_1.txt.rev.soap.PE.out||14221122||5230402||36.78|| | | ||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||P6C_1.txt.fwd.soap.PE.out||14112863||5168312||36.62(%)||70.35% | ||
|- | |- | ||
| ||P6C_1.txt.rev.soap.PE.out||14112863||4760129||33.73|| | | ||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||P7C1_1.txt.fwd.soap.PE.out||13273426||5029339||37.89(%)||72.48% | ||
|- | |- | ||
| ||P7C1_1.txt.rev.soap.PE.out||13273426||4590775||34.59|| | | ||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||P7C2_1.txt.fwd.soap.PE.out||10804019||4102770||37.97(%)||73.93% | ||
|- | |- | ||
| ||P7C2_1.txt.rev.soap.PE.out||10804019||3884944||35.96|| | | ||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||P8C_1.txt.fwd.soap.PE.out||11113577||3978002||35.79(%)||68.72% | ||
|- | |- | ||
| ||P8C_1.txt.rev.soap.PE.out||11113577||3660086||32.93|| | | ||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||P1P_1.txt.fwd.soap.PE.out||11887236||4435830||37.32(%)||71.40% | ||
|- | |- | ||
| ||P1P_1.txt.rev.soap.PE.out||11887236||4051377||34.08|| | | ||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||P2P_1.txt.fwd.soap.PE.out||10570835||3719618||35.19(%)||67.49% | ||
|- | |- | ||
| ||P2P_1.txt.rev.soap.PE.out||10570835||3414342||32. | | ||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||P3P_1.txt.fwd.soap.PE.out||12343982||4467880||36.19(%)||69.43% | ||
|- | |- | ||
| ||P3P_1.txt.rev.soap.PE.out||12343982||4103164||33.24|| | | ||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||P4P_1.txt.fwd.soap.PE.out||13306437||4612404||34.66(%)||66.16% | ||
|- | |- | ||
| ||P4P_1.txt.rev.soap.PE.out||13306437||4191194||31. | | ||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||P5P_1.txt.fwd.soap.PE.out||16356159||6335050||38.73(%)||75.05% | ||
|- | |- | ||
| ||P5P_1.txt.rev.soap.PE.out||16356159||5941194||36.32|| | | ||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||P6P_1.txt.fwd.soap.PE.out||12406211||4691026||37.81(%)||72.84% | ||
|- | |- | ||
| ||P6P_1.txt.rev.soap.PE.out||12406211||4345710||35.03|| | | ||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||P7P_1.txt.fwd.soap.PE.out||14361383||5263978||36.65(%)||71.46% | ||
|- | |- | ||
| ||P7P_1.txt.rev.soap.PE.out||14361383||4998621||34.81|| | | ||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||P8P1_1.txt.fwd.soap.PE.out||15686569||6074276||38.72(%)||74.48% | ||
|- | |- | ||
| ||P8P1_1.txt.rev.soap.PE.out||15686569||5608916||35.76|| | | ||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||P8P2_1.txt.fwd.soap.PE.out||13317181||4960421||37.25(%)||72.68% | ||
|- | |- | ||
| ||P8P2_1.txt.rev.soap.PE.out||13317181||4718163||35.43|| | | ||P8P2_1.txt.rev.soap.PE.out||13317181||4718163||35.43(%)|| | ||
|}<br> | |}<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 | {| {{table}} border = 1 | ||
Line 126: | Line 128: | ||
| align="center" style="background:#f0f0f0;"|'''Combined 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||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|| | | ||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||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|| | | ||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||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|| | | ||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||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|| | | ||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||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|| | | ||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||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|| | | ||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||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|| | | ||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||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|| | | ||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||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|| | | ||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||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|| | | ||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||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|| | | ||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||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|| | | ||P3P_1.txt.trimmed.rev.soap.PE.out||12343982||4226905||34.24(%)|| | ||
|- | |- | ||
| P4P||P4P_1.txt.trimmed.fwd.soap.PE.out||13306437||4737667||35. | | 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|| | | ||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||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|| | | ||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||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|| | | ||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||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|| | | ||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||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|| | | ||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||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|| | | ||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> | |}<br> |
Latest revision as of 09:40, 28 March 2011
Data analysis of sequencing library of Parkinson's patient samples from Burnham Institute[edit]
- Sequencing library ID: NP-220K-Parkinson_Ind1-18-Feb15, HL089 run
- Library construction: [[1]]
Sample information[edit]
Pair | Control Sample ID | Sample code | Sex | age (year.day) | Postmortem time | PD Sample ID | Sample code | Sex | age (year.day) | 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 |
DMR220k mapping by SOAP (before trimming)[edit]
Sample | Fastq file | #Mappable reads | #Mapped reads | Mapping Rate | 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(%) |
DMR220k mapping by SOAP (after trimming)[edit]
- 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)
Sample | Fastq file | #Mappable reads | #Mapped reads | Mapping Rate | 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(%) |
Sample | Correlation coefficient MinDepth=10 |
Correlation coefficient MinDepth=50 |
#of cycles | Ct value | Sample | Correlation coefficient MinDepth=10 |
Correlation coefficient 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 |
File:Capturing eff effect-2.png
Histogram plot[edit]
File:Histogram001.png File:Histogram002.png File:Histogram003.png File:Histogram004.png
DMS rate[edit]
Samples | 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% |
- Discussion with Dr. Zhang (2011_03_25)
details later......
- Rate of mapping after merging trimmed reads and use SE mapping
Sample | Fastq file | #Mappable reads | #Mapped reads | Mapping Rate | 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 |
- Correlation coefficient is pretty much the same
Sample | N | 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 |