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

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= Data analysis of sequencing library ID: NP-220K-Parkinson_Ind1-18-Feb15, HL089 run =
= Data analysis of sequencing library of Parkinson's patient samples from Burnham =
* 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]]
= DMR220k mapping by SOAP =
= DMR220k mapping by SOAP =
{| {{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||71.4
|-
| ||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||
|}<br>

Revision as of 23:51, 19 March 2011

Data analysis of sequencing library of Parkinson's patient samples from Burnham

  • Sequencing library ID: NP-220K-Parkinson_Ind1-18-Feb15, HL089 run
  • Library construction: [[1]]

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