Noi/NOTES/2011-4-16
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- Note: some pictures will be updated since need to remove the low quality samples
UPenn 48 African methylome samples data analysis[edit]
- 48 sample list: Media:48SamplelistUPenn.xlsx
- HiSeq data
- Data is deconvoluted by Dr. Zhang
- Sample sequences in different lanes were merged together, and 27 nt were trimmed from each read
- SE mapping on Triton cluster (mapped to hg18/build36 version)
- Data analysis plan by Dr. Zhang:
- Number of reads, number of CpG count, % mapping: File:UPenn48sample BSPP data analysis.xlsx
- Correlation coefficient (Dr. Zhang's script in /home/kunzhang/bin/frMethylCorr.pl and edited somepoint by Dinh): Media:frMethylCorr.xlsx
- Minidepth =10
File:UPennhcorcluster-1scriptA.png
- Then Dinh used another script to make another matrix file: details
- /home/nplongth/UPenn48_220k_20110412/trimmed_SEMapped_MethylFreq/methyl.matrix.n48_10depth.txt
- /home/nplongth/UPenn48_220k_20110412/trimmed_SEMapped_MethylFreq/methyl.matrix.n48_10depth.txt
- SE mapping on Triton cluster (mapped to hg19/build37 version)
- Number of reads, number of CpG count, % mapping:Media:UPenn48sample BSPP hg19data analysis.xlsx
- Correlation coefficient: Media:UPenn48sample hg19_frMethylCorr.xlsx