How can I visualize multiple bed files by using IGB or UCSC genome browser for ChIP peak profiling?

Question

[AndyJian]

Hi:

I have two bed files (ChIP-Seq peaks), and I want to visualize it by using IGB or UCSC genome browser. The point is, I am beginner of using genome browser to visualize genomic data. I followed UCSC genome browser user guide and learned how to load data, but can't visualize two bed files where aligning them by parallel, to visualize ChIP-Seq signal profile.

In my desired graph, I intend to get following graph (This is a just minimal example):

How can I achieve above graph if I choose three bed files as an input for UCSC genome browser or IGB? Any quick instruction to do this? Thanks in advance :)

Edit :

Here is what I got from UCSC genome browser , but did not get multiple track plot yet. How can I get my desired plot? If I need WIG files, how can I do that? Any further instruction? How can I get desired track plot either IGB or UCSC genome browser ? Any help?

[ddiez]

You added the tag R. Do you want to do this in R? In the answer is yes take a look at the Gviz package.

[AndyJian]

@ddiez: Thanks for help. I'll look over Gviz package. The point is, I could choose IGB or UCSC genome browser to get that plot. But, How can I do this directly by using UCSC genome browser? it can't allow me chose multiple track to visualize it. I am quite new to do this sort of things. How can I get track plot for three ChIP-Seq peak files? Any quick instruction that I can do it easily? Thanks

Answer 1

[Alex Reynolds]

You can either add multiple custom tracks, or if you have a web host, use a track hub: https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html

[AndyJian]

@Alex : I have bed files on my local PC, how can I upload them into UCSC genome browser server to visualize the track plot? I got lost how to do by reading the link you gave. Thank you

[Alex Reynolds]

Sounds like you don't have a web host. So upload a custom track (twice, or however many times for as many tracks as you want to upload). https://genome.ucsc.edu/goldenpath/help/customTrack.html

[AndyJian]

@Alex: I figured out loading multiple bed files, but track plot does not appear what I expected. How can I make them properly? Here is the screen shot of what I got:Here is the screenshot

[Alex Reynolds]

I don't see your tracks in the screenshot. You might check that they are correctly formatted, maybe?

[AndyJian]

@Alex: Dear Alex, I updated my post with the output of UCSC genome browser output, but still did not get multiple track that I expected. Any further assistance please? Thank you

[jotan]

That is an extremely close zoom for single nucleotide resolution. Try zooming out and/or into a region where your bed file has data. Also,

How big are your files? Can you show a few lines?

[AndyJian]

@jotan1982: Dear Jotan, sorry for my late reply. Here is my input bed files want to visualize it either by UCSC genome browser or IGB:

Here is the example

BTW, I updated my post with desired plot and output of UCSC genome browser, please check it out. Any further help on this question? Thanks in advance :)

[jotan]

The example you show, the data you want to obtain, is not a bed file.

It's a wig or a bigwig.

[AndyJian]

@Jotan: it is bed format file, each has around 10k genomic regions.

[jotan]

Sorry, I wasn't clear. I meant that the K4me3 and K27me3 examples you're showing are wig files.

Your bed files won't look like that. You need the wig version of the files.

[AndyJian]

@jotan: Dear jotan, the desired track plot I attached in this post is the just example, I took reference from other paper, I just want to get the similar plot like that. My actual data in bed format file. If I need WIG file, how can I do that? Could you please specify your motivation please? Thank you

[jotan]

Where did you get your .bed files? There are sometimes multiple formats deposited into data repositories, though this varies from study to study.

I'm not sure what you mean by 'motivation'. Do you mean the reason that I ask for a wig file? That's because you need a wig file if you want to display data like the K4me3/K27me3 tracks you show. A bed file will simply not display like that, it will display as long black horizontal bars.

[AndyJian]

@jotan1982 Thanks for your reply. The dataset I used is Myc transcription factor public data set from ENCODE project. We used MACS tools to proceed peak calling. Is there any way from bed format file to Wig ? Or any software package can do this job? Thanks for your help :)

[jotan]

Based on your limited description, I entered a MYC search into ENCODE

There's a number of file formats available. One of these is a BigWig. If you put the BigWig link into UCSC, it will display data in the way you want.

Answer 2

[Mason Meyer]

Hello jian_liangli,

My name is Mason Meyer, IGB Support Specialist. I apologize for my delay in answering your question. If I understand correctly, you wish to visualize two bed tracks with one on top of the other, correct? If this is the case, IGB should do the job well.

After starting IGB, select the genome you are working with by clicking on one of the images on the IGB Home Screen (or you could select your species and genome version from the drop-down boxes towards the upper-right of the program). Once your genome has loaded, you can open your BED files into IGB by selecting Load File from the File menu, or you can just drag-and-drop the files right onto the IGB stage.

Once your files are open in new tracks, you can select the Load Data button towards the top of IGB to load data visualizations for the region in view. The annotation tab, towards the bottom of IGB contains some additional settings that may be useful for creating the visualization you are hoping to achieve.

If you need any additional assistance, please don' hesitate to ask. Also, if you would like to share your files with us so that we can better assist you with viewing your data, feel free to contact us through our Support Page.

[AndyJian]

@Mason: Dear Mason, sorry for my late reply. Yes, you understood me correctly. I tried you suggested to me but can't get my expected track plot. I update my post with desired track plot, please check it out.

And I tried IGB to execute your suggestion, here is the screen shot:

The track plot is generated by IGB is still not desired to me. I select two bed files then load them, but can't see expected track plot yet. How can I more visually accessible that plot? How can I get my desired plot? Any further assistance please? what should I do now? Any idea?

[Mason Meyer]

Dear jian_liangli,

Sorry for my delay in responding to your comment. Based on the second IGB screenshot you sent, I can see that you have created Depth Graphs tracks from the loaded BED files. You may already be aware of this, but if you click on a track label and then select the Graph tab at the bottom of IGB, you can adjust many settings related to the Depth Graphs, including the Y-Axis Scale. If I understand your goal correctly, you should be able to produce the visualizations you are looking for by changing the Y-Axis scales for the Depth graphs.

I have attached a screenshot of two sets of depth graphs with different Y-axis scales, to help illustrate the difference. If you want your Depth Graphs to all have the same Y-Axis scale, you can hold Shift while selecting Track Labels to select more than one track at a time. If you have selected only graph tracks, you can edit the Y-Axis Scale and this will adjust the scale for all selected graphs. If this solution is still not the visualization you were hoping to achieve, please let me know and I will look for another solution.