Category Archives: chip

TIP for Mouse ChIP-seq TF profiles

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Q:
I am interested in using your probabilistic method (TIP) on some mouse ChIP-seq data. I downloaded the code (http://archive.gersteinlab.org/proj/tftarget/) , but I see that the code is very specific to human genome. As you did some analysis on the mouse TFs as well in the paper, I was wondering if you have a modified code for the mouse genome ? I would appreciate any kind of help. Thank you !

A:
Our collaborator set up a websever to tun TIP at http://syslab3.nchu.edu.tw/TIP/
You can choose to upload your data and get it run on the server. If you have many ChIP-seq files, you can download the package from the website and run it in your own computer.

Questions about chromatin data

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Q:
I would like to compare some data she has with ChIP-chip/ChIP-seq data in the worm. We have found wig files but these are not very useful. Can you direct us to a site with peak calls? (How were the peaks called?)

A:
the published worm & fly data, incl. peak calls, is at:
https://www.encodeproject.org/comparative

The peak calling is described in Boyle et al. & on the website – eg
https://www.encodeproject.org/comparative/regulation/#Humanset6

Question about RNA-Seq, HiC, ChIP-Seq data integration analysis software

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Q:
I have been searching for a bioinformatics software package that allows for the integration of different NGS analysis, RNA-Seq, HiC, ChIP-Seq in one project.

Does software like this exist yet?

A:
I don’t know of a package that can exactly help you but in some of previous work we’ve integrated RNA-seq and Chip-seq.

See links:

http://papers.gersteinlab.org/papers/worm_HM/
http://papers.gersteinlab.org/papers/tfmodel/

Code for random forest models in paper “Comparative analysis of the transcriptome across distant species”

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Q:
I read your recent letter in Nature ("Comparative analysis of the transcriptome across
distant species") and would like to use your strategy to model and predict gene expression profiles using modified histone ChIP-seq data in Eucalyptus.

Currently we have RNA-seq data for 7 tissues and some total, stranded and small RNA-seq data for selected tissues. I’m busy generating ChIP-seq profiles of 5 histone modifications in two tissues, and I’d like to see to what degree we can predict mRNA-seq data from these. We also have DNase-seq and TF ChIP-seq experiments planned in future.

I was wondering whether you have any workflows or scripts that you would be willing to share with us that would help us to better understand how the randomForest package was used for the modeling (I don’t have a programing background but we have an able bioinformatics unit). Alternatively, it would be a pleasure to collaborate on a publication with your lab if your team could assist us with the modeling aspect.

A:
There’s some scripts associated with:

http://papers.gersteinlab.org/papers/worm_HM/