Is possible to quantify the RNAPOLII levels on all the annotated genes using biwgiw files?

Question

[Lila M]

Hi everybody, I'm afraid there is no way to quantify bigwig files, but I was wondering if there is any tool or any way to quantify the levels of RNAPOLll on all the annotated genes using bigwig files (ChIP-seq, Chromatin IP against RNA Pol II).

Any suggestion will be very handy :)

Answer 1

[venu]

It's good that you already have bigwig files. Take bed file of annotated genes and use deepTools function multiBigwigSummary.

If you want to plot a metagene plot of RNApolII level over the gene, they also have functions like computeMatrix and plotProfile. If you have plans to plot, make sure to use 6 column bed file with (6th column being strand) computeMatrix so that it reverses the negative strand vectors while plotting so plot makes much more sense.

[Lila M]

Thank you for your response. I 've already used computeMatrix and plotProfile . I will try multiBigwigSummary.