Hi everyone! I'm performing some ChIP seq experiments and I want to read depth coverage over the region -500 to 3000pb of the TSS of all Ensemble protein coding transcript.
I have different approach, but as I am totally naive, I appreciate very much your advises.
a)First of all I've normalized the bam files using bamCoverage (deepTools), the output is a bedgraph, then I will do the anntotaion peak over TSS using ChIPseeker (R)
b)Also, I can do the peakannot over the bed file (after bam file conversion) and I will normalize the peakannot when I will plot it.
Other questions is, Is necessary make the peakcalling to calculate the read depth over TSS?
I'm looking forward to hear from you