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

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|-
|-
| ||P8P2_1.txt.rev.soap.PE.out||13317181||4718163||35.43||
| ||P8P2_1.txt.rev.soap.PE.out||13317181||4718163||35.43||
|}<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
|-
| ||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||74.3
|-
| ||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||35.6||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>
|}<br>

Revision as of 11:54, 22 March 2011

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: [[1]]

Sample information

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

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 71.4%
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 32.3
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 31.5
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


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
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 74.3
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 35.6 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