Dear all, we have observed an interesting behaviour when it comes to the bigWig file generation in both the ChIP-seq as well as CUT&RUN workflow, and I wanted to open this up to your collective input. The ChIP-seq pipeline runs the following code to generate bigWig files:

bedtools genomecov \
    -ibam H3K27me3.mLb.clN.sorted.bam \
    -bg \
    -scale $SCALE_FACTOR \
    -pc \
    | sort -T '.' -k1,1 -k2,2n > H3K27me3.bedGraph

bedGraphToBigWig \
    H3K27me3.bedGraph \
    Homo_sapiens.GRCh38.dna.primary_assembly.fa.sizes \
    H3K27me3.bigWig

This default behaviour creates bigWig files that appear to have a relatively high level of background. When using the option

--bga

(instead of

--bg

), uncovered bins get assigned values of 0 and are not skipped. This appears to result to lower levels of background, which is more pleasing to the eye in IGV: