I have downloaded several ChIP-seq data (histone marks) and I'm trying to plot their coverage over the TSS
Since every file comes from a different sequencing experiment the sequencing depth varies from one sample to another. Therefore, what I'm trying to do is scale all the samples by a specific value.
The deeptools package offers that via the bamCompare --scaleFactor function. Is it sensible to calculate the mean coverage for each sample and then apply a scaling factor to normalise all the bam files to each other?
Moreover, I'm having trouble parsing the matrix file from the computeMatrix function into R. If anyone is familiar with deeptools any explanations with regard to what the matrix files represent would be much appreciated