mohamedomar2020 / prostate_medipseq

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.

• Alignment to hg19: STAR v2.7.8a

• Fastq quality control: FASTqc

• BAM quality control: qualimap v.2.2.2-dev

• Analysis tools: MEDIPS and qsea (R) - macs3 (command line)

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For macs3:

• Bedgraph to bigwig: ucsc-bedgraphtobigwig v4

Note: Chromosome sizes file can be downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/latest/

• Convert the annotation gtf to bed file: convert2bed v: 2.4.39

• Bed annotation: bedmap v2.4.39

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Further analysis and visualization:

annotatr and Gviz (R)