can anybody please tell me how to implement the logistic regression on chip seq data after extracting features like distance from tss and peak breadth and peak count
You can do it in R with the glm function. If you google around, you will find many examples of such regressions.
please tell me how to give input file
This is going to be hard if you don't know how to use R because it takes a bit of learning. Alternatively, doing a logistic regression is also possible with Excel.
If you want to stick with R, you can usually load any kind of text data using read.table().