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LD Score Regression (LDSC)
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Celltype/tissue specific analysis on ATAC seq data #200

Open prashanthsama1 opened 4 years ago

prashanthsama1 commented 4 years ago

Hi,

I am trying to run celltype/tissue specific analysis as mentioned in the tutorial on ATAC-seq data.

I obtained narrowPeak files from MACS2. I was wondering how to approach from there to perform celltype/tissue specific analysis. I have the following questions.

  1. Should we calculate t-statistic for ATAC seq peak files or can we consider the peak files themselves as tissue/celltype specific set. If we have to calculate t-statistic, then how to calculate the t-stats as each peak file has different regions.

  2. How to define a control set in this case.

  3. When we have multiple peak files from the same celltype/tissue, should we just combine those files or is there any specific way to merge them?

It would be great if you can provide any example on this.

Thanks..!!!!

HelloWorldLTY commented 1 year ago

Hi, sorry to disturb you. Could you please share where did you find the tutorial on ATAC-seq data? Thanks a lot.