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How to set up infrastructure for ChIP-seq analysis using the Biostars Handbook 2nd edition according to Ming Tangs Guide.

Setting up the folder structure

Go to the directory for ChIP-seq with your analysis

cd ~/work/ChIP-seq_<analysis-name>
mkdir {data,results,scripts,software}
mkdir -p results/{bams,peaks,fastqc,motifs}
cd data
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Download data

Get the annotation list from the sra run selector

IDs.txt
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Prefetch and convert files to fastq

Go into the ~/work/ChIP-seq_/data

time parallel -j 10 'prefetch {}' :::: IDs.txt
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time parallel -j 10 'fasterq-dump {}/{}/sra --split-files --threads 6 :::: IDs.txt
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