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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 = * 48 sample list: [[Media:48SamplelistUPenn.xlsx]]<br> * 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]]<br> * Correlation coefficient (Dr. Zhang's script in /home/kunzhang/bin/frMethylCorr.pl and edited somepoint by Dinh): [[Media:frMethylCorr.xlsx]]<br> * Minidepth =10<br> [[File:UPennhcorcluster-1scriptA.png| 1000px]]<br> * Then Dinh used another script to make another matrix file: details ** /home/nplongth/UPenn48_220k_20110412/trimmed_SEMapped_MethylFreq/methyl.matrix.n48_10depth.txt<br> [[File:UPennhcorcluster-2B.png| 1000px]]<br> ** SE mapping on Triton cluster (mapped to hg19/build37 version) * Number of reads, number of CpG count, % mapping:[[Media:UPenn48sample BSPP hg19data analysis.xlsx]]<br> * Correlation coefficient: [[Media:UPenn48sample hg19_frMethylCorr.xlsx]]<br>
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