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

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* Sequencing library ID: '''NP-220K-Parkinson_Ind1-18-Feb15, HL089 run'''
* 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]]
* Library construction: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-2-15]]
== Sample information ==
{| {{table}} border = 1
| align="center" style="background:#f0f0f0;"|'''Pair'''
| align="center" style="background:#f0f0f0;"|'''Control Sample ID'''
| align="center" style="background:#f0f0f0;"|'''Sample code'''
| align="center" style="background:#f0f0f0;"|'''Sex'''
| align="center" style="background:#f0f0f0;"|'''age (year.day)'''
| align="center" style="background:#f0f0f0;"|'''Postmortem time'''
| align="center" style="background:#f0f0f0;"|'''PD Sample ID'''
| align="center" style="background:#f0f0f0;"|'''Sample code'''
| align="center" style="background:#f0f0f0;"|'''Sex'''
| align="center" style="background:#f0f0f0;"|'''age (year.day)'''
| align="center" style="background:#f0f0f0;"|'''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
|}<br>
= DMR220k mapping by SOAP =
= DMR220k mapping by SOAP =
{| {{table}} border = 1
{| {{table}} border = 1

Revision as of 01:00, 20 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]]

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