Noi/NOTES/2011-3-17
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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 |