Noi/NOTES/2011-3-17: Difference between revisions
Jump to navigation
Jump to search
>Noi No edit summary |
>Noi No edit summary |
||
Line 2: | Line 2: | ||
* 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 |