Noi/NOTES/2011-3-29

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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