Noi/NOTES/2011-3-29
Jump to navigation
Jump to search
Data analysis of sequencing library of PBelmonte's samples (Guanghui's project) from Salk Institute
- Sequencing library ID: Sequencing library ID: NP-220K-Belmonte_Ind8-12-March10, HL091 run
- Library construction: [[1]], [[2]]
Sample information
DMR220k mapping by SOAP (trimmed 10bp from 5' end)
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
Sample | MinDepth=10 | N | MinDepth=20 | N | MinDepth=50 | N |
1. HGPS | 0.958 | 15100 | 0.969 | 8070 | 0.981 | 2715 |
2. cHGPS1 | 0.959 | 13741 | 0.973 | 6591 | 0.983 | 1668 |
3. cHGPS40 | 0.963 | 14627 | 0.974 | 7432 | 0.984 | 2225 |
4. AWS | 0.965 | 15197 | 0.973 | 7929 | 0.983 | 2279 |
5. cAWS1 | 0.915 | 12752 | 0.939 | 6503 | 0.96 | 1937 |
Histogram plot
File:Guanghui his-1.png File:Guanghui his-2.png
File:Guanghui-hcorcluster-1.PNG