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
**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 |