Noi/NOTES/2011-3-29: Difference between revisions
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= Data analysis of sequencing library of | = Data analysis of sequencing library of Belmonte's samples (Guanghui's project) from Salk Institute = | ||
* Sequencing library ID: ''' Sequencing library ID: ''NP-220K-Belmonte_Ind8-12-March10, HL091 run''' | * Sequencing library ID: ''' Sequencing library ID: ''NP-220K-Belmonte_Ind8-12-March10, HL091 run''' | ||
* Library construction: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-3-10]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-3-18]] | * Library construction: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-3-10]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-3-18]] | ||
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| ||cAWS1.txt.trimmed.rev.soap.out||11800686||4358910||36.94%|| | | ||cAWS1.txt.trimmed.rev.soap.out||11800686||4358910||36.94%|| | ||
|}<br> | |}<br> | ||
== Correlation coefficient == | == Correlation coefficient == | ||
{| {{table}} border = 1 | {| {{table}} border = 1 | ||
| align="center" style="background:#f0f0f0;"|'''Sample''' | | align="center" style="background:#f0f0f0;"|'''Sample''' | ||
| align="center" style="background:#f0f0f0;"|'''MinDepth=10''' | |||
| align="center" style="background:#f0f0f0;"|'''N''' | |||
| align="center" style="background:#f0f0f0;"|'''MinDepth=20''' | |||
| align="center" style="background:#f0f0f0;"|'''N''' | |||
| align="center" style="background:#f0f0f0;"|'''MinDepth=30''' | |||
| align="center" style="background:#f0f0f0;"|'''N''' | |||
| align="center" style="background:#f0f0f0;"|'''MinDepth=50''' | |||
| align="center" style="background:#f0f0f0;"|'''N''' | | align="center" style="background:#f0f0f0;"|'''N''' | ||
|- | |- | ||
| 1. HGPS||15100||0. | | 1. HGPS||0.958||15100||0.969||8070||0.974||5258||0.981||2715 | ||
|- | |- | ||
| 2. cHGPS1||13741||0. | | 2. cHGPS1||0.959||13741||0.973||6591||0.977||3877||0.983||1668 | ||
|- | |- | ||
| 3. cHGPS40||14627||0. | | 3. cHGPS40||0.963||14627||0.974||7432||0.978||4584||0.984||2225 | ||
|- | |- | ||
| 4. AWS||15197||0. | | 4. AWS||0.965||15197||0.973||7929||0.977||4762||0.983||2279 | ||
|- | |- | ||
| 5. cAWS1||12752||0. | | 5. cAWS1||0.915||12752||0.939||6503||0.949||4159||0.96||1937 | ||
|}<br> | |}<br> | ||
== Histogram plot == | == Histogram plot == | ||
[[File:Guanghui his-1.png]] [[File:Guanghui his-2.png]]<br> [[File:Guanghui-hcorcluster. | * MinDepth = 10 | ||
[[File:Guanghui his-1.png]] [[File:Guanghui his-2.png]]<br> [[File:Guanghui-hcorcluster-1.PNG]] | |||
* Note: Since the quality of cAWS1 sample was lower than other samples, Dr. Zhang suggest me to in crease the minimal read depth for this sample to make the correlation coefficient comparable to other sample. And also do clustering analysis only on the sites that are present in all five lines | |||
== Histogram plot == | |||
* MinDepth = 20 | |||
[[File:cAWS1Depth20histogram-1-head.png]] [[File:cAWS1Depth20histogram-2-head.png]] [[File:cAWS1Depth20hcorcluster-head.png]] | |||
* MinDepth = 30 | |||
[[File:cAWS1Depth30histogram-1-head.png]] [[File:cAWS1Depth30histogram-2-head.png]] [[File:cAWS1Depth30hcorcluster-head.png]] | |||
* MinDepth = 50 | |||
[[File:cAWS1Depth50histogram-1-head.png]] [[File:cAWS1Depth50histogram-2-head.png]] [[File:cAWS1Depth50hcorcluster-head.png]] |
Latest revision as of 01:25, 7 April 2011
Data analysis of sequencing library of Belmonte's samples (Guanghui's project) from Salk Institute[edit]
- Sequencing library ID: Sequencing library ID: NP-220K-Belmonte_Ind8-12-March10, HL091 run
- Library construction: [[1]], [[2]]
Sample information[edit]
DMR220k mapping by SOAP (trimmed 10bp from 5' end)[edit]
Sample ID | Fastq file | #Mappable reads | #Mapped reads | Mapping Rate | Combined Mapping Rate |
1. HGPS | HGPS.txt.trimmed.fwd.soap.out | 14499233 | 6347271 | 43.78% | 80.85% |
HGPS.txt.trimmed.rev.soap.out | 14499233 | 5375045 | 37.07% | ||
2. cHGPS1 | cHGPS1.txt.trimmed.fwd.soap.out | 10081073 | 4325613 | 42.91% | 79.42% |
cHGPS1.txt.trimmed.rev.soap.out | 10081073 | 3680896 | 36.51% | ||
3. cHGPS40 | cHGPS40.txt.trimmed.fwd.soap.out | 11993449 | 5239070 | 43.68% | 80.65% |
cHGPS40.txt.trimmed.rev.soap.out | 11993449 | 4434208 | 36.97% | ||
4. AWS | AWS.txt.trimmed.fwd.soap.out | 12099285 | 5238933 | 43.30% | 80.04% |
AWS.txt.trimmed.rev.soap.out | 12099285 | 4444701 | 36.74% | ||
5. cAWS1 | cAWS1.txt.trimmed.fwd.soap.out | 11800686 | 5172733 | 43.83% | 80.77% |
cAWS1.txt.trimmed.rev.soap.out | 11800686 | 4358910 | 36.94% |
Correlation coefficient[edit]
Sample | MinDepth=10 | N | MinDepth=20 | N | MinDepth=30 | N | MinDepth=50 | N |
1. HGPS | 0.958 | 15100 | 0.969 | 8070 | 0.974 | 5258 | 0.981 | 2715 |
2. cHGPS1 | 0.959 | 13741 | 0.973 | 6591 | 0.977 | 3877 | 0.983 | 1668 |
3. cHGPS40 | 0.963 | 14627 | 0.974 | 7432 | 0.978 | 4584 | 0.984 | 2225 |
4. AWS | 0.965 | 15197 | 0.973 | 7929 | 0.977 | 4762 | 0.983 | 2279 |
5. cAWS1 | 0.915 | 12752 | 0.939 | 6503 | 0.949 | 4159 | 0.96 | 1937 |
Histogram plot[edit]
- MinDepth = 10
File:Guanghui his-1.png File:Guanghui his-2.png
File:Guanghui-hcorcluster-1.PNG
- Note: Since the quality of cAWS1 sample was lower than other samples, Dr. Zhang suggest me to in crease the minimal read depth for this sample to make the correlation coefficient comparable to other sample. And also do clustering analysis only on the sites that are present in all five lines
Histogram plot[edit]
- MinDepth = 20
File:CAWS1Depth20histogram-1-head.png File:CAWS1Depth20histogram-2-head.png File:CAWS1Depth20hcorcluster-head.png
- MinDepth = 30
File:CAWS1Depth30histogram-1-head.png File:CAWS1Depth30histogram-2-head.png File:CAWS1Depth30hcorcluster-head.png
- MinDepth = 50
File:CAWS1Depth50histogram-1-head.png File:CAWS1Depth50histogram-2-head.png File:CAWS1Depth50hcorcluster-head.png