Correlating ATAC-seq peak files (.bed) with Hi-C data

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Diana Qi

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Sep 14, 2017, 1:52:14 PM9/14/17
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Hi all,

I am new to bioinformatics, especially with the Hi-C data processing. Now I have two ATAC-seq peak files in bed format, with the first column of chromosome names, the second column of start sites and the third column of end sites. I want to analyze a Hi-C dataset with these ATAC-seq peak files, i.e. to visualize the interaction frequency between the ATAC peak sites. I have no idea how I can possibly do it (what tools to use? what script to follow?) and would appreciate it if anyone could kindly provide me with some advice.

Thanks,
Diana

Neva Durand

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Sep 14, 2017, 2:04:43 PM9/14/17
to Diana Qi, 3D Genomics
Hello Diana,

I would start by looking at some Hi-C datasets in Juicebox and loading your ATAC-seq tracks as 1D tracks alongside the maps.  If you have a specific Hi-C dataset that you've created, you can run Juicer to process it into a .hic file and load that into Juicebox.  Otherwise, you can look at the menu in Juicebox where there are various maps from many different cell types available.

Here is some more information to get you started with Juicebox:

You can also access Juicebox on the web, here: 

I always find it best to visualize first, in order to develop hypotheses; then you can confirm or deny the hypotheses with further analysis (for example via intersecting your tracks with peaks or domains, or other features that you see in the data).

Best
Neva

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Neva Cherniavsky Durand, Ph.D.
Staff Scientist, Aiden Lab

Diana Qi

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Sep 14, 2017, 2:36:43 PM9/14/17
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Hi Neva,

I visualized the .hic dataset in the online juicebox with the ATAC files loaded as tracks. It seemed like there were interactions between many of the peak sites. The next thing that I am thinking that might be worth doing is to statistically determine the percentage of sites that have the interactions. Are there any available software that can possibly do this?

Thanks,
Diana

在 2017年9月14日星期四 UTC-4下午2:04:43，Neva Durand写道：
Hello Diana,

I would start by looking at some Hi-C datasets in Juicebox and loading your ATAC-seq tracks as 1D tracks alongside the maps.  If you have a specific Hi-C dataset that you've created, you can run Juicer to process it into a .hic file and load that into Juicebox.  Otherwise, you can look at the menu in Juicebox where there are various maps from many different cell types available.

Here is some more information to get you started with Juicebox:

You can also access Juicebox on the web, here: 

I always find it best to visualize first, in order to develop hypotheses; then you can confirm or deny the hypotheses with further analysis (for example via intersecting your tracks with peaks or domains, or other features that you see in the data).

Best
Neva
On Thu, Sep 14, 2017 at 1:52 PM, Diana Qi <laven...@gmail.com> wrote:
Hi all,

I am new to bioinformatics, especially with the Hi-C data processing. Now I have two ATAC-seq peak files in bed format, with the first column of chromosome names, the second column of start sites and the third column of end sites. I want to analyze a Hi-C dataset with these ATAC-seq peak files, i.e. to visualize the interaction frequency between the ATAC peak sites. I have no idea how I can possibly do it (what tools to use? what script to follow?) and would appreciate it if anyone could kindly provide me with some advice.

Thanks,
Diana

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Neva Durand

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Sep 14, 2017, 2:52:48 PM9/14/17
to Diana Qi, 3D Genomics
Hi Diana,

You could try bedtools.  The format for 2D annotations is very similar to bedpe (if not identical), so you could take peaks and domains files from published datasets, or your own dataset, and intersect it with the ATACseq.  Here's a link I found:  http://bedtools.readthedocs.io/en/latest/content/tools/pairtopair.html

Best
Neva

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