Question: (Closed) What are the different approaches for reanalysis of chipseq and RNAseq data from GSE
gravatar for macmath
5.0 years ago by
macmath140 wrote:

1) Define genome promoter occupancy of Transcription Factor (distinguished shared versus specific binding of the components).

2) Combine data from TF binding with RNA-seq data and identify a set of gene directly controls by TF

3) Define the binding motif as the potential transcription factors that may interact with TF

4) Define TF promoter/enhancer bindings onto these genes (genome browser)

rna-seq chip-seq • 1.2k views
ADD COMMENTlink written 5.0 years ago by macmath140

Hello macmath!

We believe that this post does not fit the main topic of this site.

This isn't a question.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.


ADD REPLYlink written 5.0 years ago by karl.stamm3.9k

My question was based for the broader young bioinformaticians, as I am one of them I would like to know how other bioinformaticians re-analyse chipseq and RNAseq data from GSE. Everyone use their own workflow adapting to the data they receive and as we do not have any gold-standards I thought asking in the forum would help. The focus of the query was to know what would be their workflows and how do they address questions like defining promoter occupancy of a specific transcription factor, combing data (Chip-seq and RNAseq) to identify genes directly controlled by transcription factor, defining binding motif, enhancer bindings etc Hope you could suggest some alternatives as you are expert in R analysis and have created packages in Bioconductor. Thank you in advance. Cheers!

ADD REPLYlink written 5.0 years ago by macmath140

But this is too broad question and Too many questions. If you split each question, you will find many posts in biostars. And as you said, its tru that "Everyone use their own workflow adapting to the data they receive".

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by geek_y11k
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