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Ns126:Encode Methylation
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==RRBS Data Analysis to Encode Project (Bed/MethylFreq)== ===Data Download=== Fastq and bed files can be downloaded from Encode Project. 101 RRBS data (bed files) were downloaded. 2,646,999 CpG loci were covered by 101 RRBS data while 866,979 CpG loci (32.8%) were detected in at least 80% samples. * File Download cd /home/shg047/oasis/monod/rrbs_encode wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethylRrbs/files.txt wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibMethylRrbs/md5sum.txt perl fastqDownloadRRBSEncode.pl files.txt *bed11 to bedGraph cd /home/shg047/oasis/monod/rrbs_encode for i in `ls *bed.gz` do zcat $i | grep -v "^track" |sort -k1,1 -k2,2n | awk '$5>9 {print $1"\t"$2"\t"$3"\t"$11}'> $i.bedGraph done *Pearson Correlation cd /home/shg047/oasis/monod/rrbs_encode
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