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 |