I would like to know how to perform this global Pol II occupancy which is shown here:
So in this figure they are analysing the Pol II occupancy in Control,PAF1 KD and LEO1.
I have similar data.
In order to determine whether PAF1 has a direct effect on the regulation of Pol II at the promoter-proximal region, ChIP-seq was performed. Heatmaps ranked by decreasing Pol II occupancy show a positive correlation with PAF1 and Pol II (Figure 1G). To corroborate these findings, we also performed ChIP-seq with LEO1, as this was the only other antibody that we tested that gave any significant ChIP-seq signal. Like PAF1, LEO1 is found throughout gene bodies with particular enrichment around the TSS (Figure 1G). Interestingly, LEO1 was not broadly lost from chromatin upon PAF1 knockdown, but the distribution was altered, including reduced occupancy in the promoter-proximal region
So what I have done so far in terms of analysis is I did peak-calling using homer for my control and KD condition along with their Pol II chip.I was going for this differential binding analysis but this is now how i Pol II data is done after reading the paper I got. In homer there is this function analyzeRepeats.pl which is provided in this section Measuring Gene Expression in Exons vs. Gene Bodies. telling genes (default) - Counts tags on the full gene body (TSS to TTS).This is useful for GRO-Seq where we expect coverage across the entire transcript.Can also be used to quantify H3K36me3 or PolII ChIP-Seq.
How do I proceed and what tool should I use to show the Pol II occupancy at different condition and as of now I don't have respective rna seq data, do i need expression data of genes to perform occupancy analysis.