Recently, I have read "Gcn4 Binding in Coding Regions Can Activate Internal and Canonical 5 0 Promoters in Yeast". However, I did not understand how they did the normalization for the ChIPseq and RNAseq.
For ChIPseq "Gcn4 occupancy proﬁles were obtained from the alignment (.bam) ﬁles using the bioinformatics toolbox from MATLAB. To allow the comparison between different samples, each proﬁle was normalized such that the average occupancy for each chromosome was equal to one."
For RNAseq "RNA reads are normalized by combining all reads on both DNA strands for genes on the same chromosome and setting the average read density per nucleotide to one."
Because they did the strand-specific RNAseq so they need to combine all read on both DNA strands for genes.
Can anyone help me?