Profile of multiple bigwigs

[Alexandre Maia]

Hi,

I have been using your tools extensively, and I really like them. 

I do have a suggestion/comment:

I have been trying to plot profiles of different BigWigs in the same region (Bed file) and coundn't not find a way to do it. I'm sure it shouldn't be too hard to do it.

Thanks.

Alexandre Gaspar-Maia, PhD

[Friederike Dündar]

Hi Alexandre,

thanks for your feedback!

At the moment, when faced with a wish like yours, we are using the following approach:

1. run computeMatrix and profiler with all bigWig files with the --outFileData option to obtain the values underlying the summary plots (if the order is important for a heatmap, you can save the ordered bed-file using the --outFileSortedRegions options on the command line or via the extended output options in Galaxy and use that for subsequent runs)

2. use an R script to combine the different summary plot files into one plot

If you are a little bit familiar with R, I could send you the script which is fairly straight-forward to use. That being said, the handling of multiple bigWig files is definitely on our to-do list!

Best wishes,

Friederike

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[Maddie]

Hi,

I recently started using deepTools and have recommended it to several people. Very nice profiler and heatmapper tools and the image quality and color combinations are great. I was wondering if I can get that R script you mention below to combine different summary plots into one. I'd appreciate it a lot.

Thanks,

Maddie

[Elena Gómez-Díaz]

Hi Friederike,

I just have a similar issue and I would be more than happy and very thankful if you can send me the R script.

Thanks!

El dimecres 26 de febrer de 2014 14:51:19 UTC-5, Friederike Dündar va escriure:

[Friederike Dündar]

Hi Elena,

I just realized that I didn't forward the reply to the mailing list, so here is what I sent out a couple of days ago:

I uploaded the scripts to my github account: https://github.com/friedue/randomScripts/tree/master/deepTools
One contains the functions you will need (which you will hopefully not have to modify), the other one is a simple R workflow which you will have to modify with your parameters and files. I hope that the comments in the script are useful enough to make it work, otherwise don't hesitate to get back to me.

However, instead of using these scripts, I highly recommend to have a look at the developmental version of multi-bigWig-deepTools which you can use to generate heatmaps and profiles for an arbitrary number of bigWig files.
You can find the branch here: https://github.com/fidelram/deepTools/tree/multiheatmapper
And this is how you clone it: git clone -b multiheatmapper https://github.com/fidelram/deepTools.git
Then just install it the same way as you installed the published deepTools version.

Cheers,

Friederike

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[guswa...@gmail.com]

Hello Friederike

Thanks for sharing your R-script
Unfortunately I'm getting the following error after I run PlottingSummaryPlots()

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
line 1 did not have 306 elements

I'm trying to plot the Matrix outputs from two different bigwig files. The bed file is identical for both bigwig files.
Any idea why this is happening?

Cheers
Constantine

[Friederike Dündar]

Most likely, some issue with the number of columns or the type of field separator.

If you don't mind, you could send me the files privately and I can have a look.

Do note though that the latest release of deepTools offers the possibility to plot the profiles/heatmaps for multiple bigwig files. You can find it here: https://github.com/fidelram/deepTools/tree/release-1.6

Best,

Friederike