The BAM files used for the tests and example code have been taken from the original CRUP publication (Ramisch et al., 2019). The test data can be found on the git repository for CRUP (https://github.com/VerenaHeinrich/CRUP) and are deposited in https://github.com/VerenaHeinrich/CRUP/tree/master/TEST/DATA/ChIPseq . To cut down on disk space and run time, the BAM files have been further reduced to only contain reads in region chr8:26,841,601-26,847,600. The region was saved in the BED3 format and intersectBed by BEDtools was used to filter the reads. Here is an example code snippet:
intersectBed -abam ~/Condition1.H3K4me3.bam \
             -b ~/region.bed > ~/Condition1_reduced.H3K4me3.bam
 region.bed is a file in BED format that contains the region for which the reads should be kept. It can be generated by creating a tab-separated text file containing following line:
 8	26841601	26847600
 
For the gene expression counts, the RNA-seq data was taken from https://github.com/VerenaHeinrich/CRUP/tree/master/TEST/DATA/RNAseq. The reads outside region chr8:1-129,401,200 were filtered using intersectBED. The code for this is the same as for the ChIPseq BAM files, but the BED file with the region of interest contains the adjusted coordinates:
chr8	1	129401200
