Chip Seq Peaks/ Enrichment Profilig?

Question

[morovatunc]

Hello all,

I was told to obtain a chip seq peak figure from one of the articles (http://www.cell.com/cancer-cell/abstract/S1535-6108(12)00489-8). Figure 1B. My following questions might be dumb but even though I know some stuff about this workflows, this terminology usually creates a glitch on my mind. Before asking questions, I would like to explain that what I did so far.

1. I downloaded chip seq data (BED files)
2. Ran macs14 peak calling workflow. There are control files of the each unique run. (Like GSM698575_7_ChIP.bed and GSM698575_7_ChIP_Input.bed) Therefore instead of omitting the control in macs14, I entered this control bed file too.

3. I got macs output(below) and optional ( bed graph or wig file). I ran it two times to see the difference btw bedgraph( I transform to bigwig with kentutils) and wig files. ***If I go with the bed graphs, I have to use kent utils to clip my beds then transform to bigwig with bedgraphtoBigWig.

   macs14_MACS_bedGraph
   macs14_diag.xls
   macs14_model.pdf
   macs14_model.r
   macs14_negative_peaks.xls
   macs14_peaks.bed
   macs14_peaks.xls
   macs14_summits.bed
   

I couldn't get a similar graph in the figure 2. ( I know that this paper called the peaks with SWEMBL). So,

My Questions are:

1. Shouldn't I get similar peaks as figure 2
2. What additional step I should do?
3. My cannot observe same graphs with bed graph and wigs. Why can I get the same graph ? Which file type should be my input of IGV?
4. Was using control wrong?

Any advice will be priceless for me. Thank you for your help and patience for reading this post.

Tunc

[dally]

I'm rather new so I can't help with much.

But 4) You should be using .bigwig files to load into IGV.

Answer 1

[Ming Tommy Tang]

check my github page https://github.com/crazyhottommy/ChIP-seq-analysis. You might find what you want.

[dally]

I just want to personally say that your github was so helpful.

[morovatunc]

I have already cloned your github. It is very useful. However, I require little bit explanation about the methods. Like general concept. I feel like thrown in the deep sea when I see that many programs around.

[Ming Tommy Tang]

I have linked many papers in the githhub page. Make sure you read them first.