occupancy at common specific TF binding sites

Question

[woongjaej]

Hi, I'm a newbie at analysing ChIP-seq and I have some question.

1. I want to draw a picture which shows tag density as the number of tags per 100bp for example. And these tag density drawn form the centre of each 'some specific TF' binding site. I tried to find out very hard but failed. Maybe because of my poor English...

2. How can I draw a picture like log2(enrichment over input)??Like, may I use the value 'pileup' from the MACS2 output??

Maybe these questions are silly for the experts... This is my first time using "Biostar" board and if I wrote something wrong or did something wrong, please let me know.

Any advises or example methods will be a great help.. Please help me out a little.

Thank you. Best, Woongjae

Answer 1

[Kevin Blighe]

Hi, you may want to take a look at this thread: Visualization for ChIP-seq analysis

Best of luck Woongjae

Kevin

[woongjaej]

Hi Kevin,

Thank you for your kind reply.

By the way, can the plotHeatmap command can draw tag density plot, too?? And the document ex) is for histone ChIp-seq, but are there any example for TF ChIP-seq that I can get some tips from?

Thank you very much.

Woongjae

[Kevin Blighe]

Hi Woongjae, the plotting functions will work for any type of ChIP data, whether TF or broad peak regions. These functions typically accept bedgraph files that have already been processed and have peaks identified.

plotHeatmap should be fine for TF, as far as I know.

[woongjaej]

Thanks for the kind reply.

Thank you very much Kevin!