Question: Assigning nucleosome peaks to transcription factor bound locations(obtained by ChIP-seq)
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gravatar for sshibin
7 months ago by
sshibin0
sshibin0 wrote:

Hi everyone, I have two datasets (mapped to mm10 and peak called). 1. Nucleosome positions in progenitor cells (obtained by MNAse seq) 2. Transcription factor binding positions in the same cells (obtained by ChIP-seq)

I have been able to do analysis individually on these, for example, assigning nucleosome peaks to the nearest TSS and looking for promoter and enhancer specific patterns. With ChIP-seq datasets, I was able to find genes associated to the TF peaks and how it impacts gene expression using RNA-seq dataset. I did all this using R.

Now, I am interested to know the nucleosome positions (MNase-seq) relative to the TF binding site (ChIP-seq). It should be something similar to what I did for TSS. But I am not able to figure out a standard way to approach this. This is how I tried to do to assign peaks to promoters and visualize it. But it will be definitely different I suppose.

promoter <- getPromoters(TxDb=txdb, upstream=300, downstream=300
  tagMatrixDay5nuc <- getTagMatrix(Day5_nuc_500bp, windows=promoter)
  plotAvgProf(tagMatrixDay5nuc, xlim=c(-300, 300), 
            ylab = "Read Count Frequency")

Will TFBStools help? Or is there another package to do this? I used nucleR and ChIPseeker packages. I am not much experienced in R, only few months into this. Thanks in advance!

ADD COMMENTlink written 7 months ago by sshibin0
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