Incorporating input control data

Generate sample files for minimal example: Show/Hide

Beside the target PUM2 eCLIP data, we download the corresponding preprocessed input data from ENCODE, and again filter the paired-end data to keep only R2:

wget -O input.aligned.prepro.bam https://www.encodeproject.org/files/ENCFF043ERY/@@download/ENCFF043ERY.bam
samtools view -hb -f 130 input.aligned.prepro.bam -o input.aligned.prepro.R2.bam
samtools index input.aligned.prepro.R2.bam

PureCLIP

To run PureCLIP with input control data, additionally hand over the (preprocessed) BAM file from the input experiment with -ibam and the associated BAI file with -ibai:

pureclip -i aligned.prepro.R2.bam -bai aligned.prepro.R2.bam.bai -g ref.hg19.fa -iv 'chr1;chr2;chr3;' -nt 10 -o PureCLIP.crosslink_sites.cov_inputSignal.bed -ibam input.aligned.prepro.R2.bam -ibai input.aligned.prepro.R2.bam.bai