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BETA for different conditions

HI! I have ChIP-seq data from two different conditions (stressed and non-stressed cells with overexpression of a TF), and RNA-seq data from those conditions and in two type of cells: WT and overexpressed. Is it possible to use BETA software to integrate these data and compare both conditions? Thank you so much for your help! This is the best group ever!

rna-seq chip-seq

Probably yes. For a more elaborate answer we need details which you currently do not provide.

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