Binning approach and normalization

After mapping of the sequencing reads to the human genome, bam files were converted to bed using bedtools’ (v2.29.2) “bamtobed” and only sequence chromosome and start information retained. Optional: split files by chromosome for better handling. (example files: chr1.input_start.bed, chr1.chip_start.bed)

Define bin size (e.g.: 10kb, chromosome size information necessary) and count the number of reads within each bin (function: 01_countReadFrequency_example.R). Optional: Index files to remove bins without reads later on.

For normalization by input, keep bins > 0 in input. Match bins in chip files and divide ChIP read frequency by input read frequency. Apply normalization by mean ChIP read frequency (function: 02_inpDiv_normByMean.R)

The resulting files contain the index of the bin and the normalized read frequencies.

Upload files: 

hg19_chrSizes.bed

chr1.input_start.bed 

chr1.chip_start.bed

01_countReadFrequency_example.R

02_inpDiv_normByMean.R