Noi/NOTES/2011-3-17: Difference between revisions

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[[File:histogram003.png]]
[[File:histogram003.png]]
[[File:histogram004.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]]
[[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>

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%


File:Hcorcluster.PNG

  • 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