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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