This repository contains the scripts used to analyze the MEDIP-seq data from PKCI KO (sgPKCI) versus WT (sgC) samples from prostate c42b cell line.
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Alignment to hg19: STAR v2.7.8a
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Fastq quality control: FASTqc
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BAM quality control: qualimap v.2.2.2-dev
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Analysis tools: MEDIPS and qsea (R) - macs3 (command line)
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- Bedgraph to bigwig: ucsc-bedgraphtobigwig v4
Note: Chromosome sizes file can be downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/latest/
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Convert the annotation gtf to bed file: convert2bed v: 2.4.39
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Bed annotation: bedmap v2.4.39
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annotatr and Gviz (R)