Chip Seq Peaks/ Enrichment Profilig?
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5.5 years ago
morovatunc ▴ 470

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 omiting 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 couldnt 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

ChIP-Seq next-gen seq • 2.0k views
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5.5 years ago
Ming Tang ★ 2.6k

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

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

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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.

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

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5.5 years ago
dally ▴ 190

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

 

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

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