Preprocessing Dnase file

Preprocessing of DNase-Seq datasets: Dataset Assay Link

HEK293T DNA accessibility DNase-Seq wgEncodeOpenChromDnaseHek293tPk

unzip file using:

gunzip w wgEncodeOpenChromDnaseAdultcd4th1Pk.narrowPeak.gz

compress file

bgzip -c w wgEncodeOpenChromDnaseAdultcd4th1Pk.narrowPeak > wgEncodeOpenChromDnaseAdultcd4th1Pk.narrowPeak.gz

Indexing using:

tabix -p bed w wgEncodeOpenChromDnaseAdultcd4th1Pk.narrowPeak.gz

Preprocessing of the crisper targets file turning it to tsv format. Calculation of intersection Go over each target in targets file and query it using tabix:

tabix wgEncodeOpenChromDnaseAdultcd4th1Pk.narrowPeak.gz chr1:713835-714424

save results to new csv file with intersection results

Preprocessing targets file

Narrow peak

**chrom **	**chromStart **	**chromEnd **	**name **	**score **	**strand **	**upstrea **	**protospacer **	**PAM **	**downstream **	signal_value_dnase

Dataset	Assay	Link
HEK293T DNA accessibility	DNase-Seq	ENCFF774HUB.bam
U2OS DNA accessibility	DNase-Seq	SRR4413990.fastq

calculate intercection