Heatmap using publicly available Chip-Seq data
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You will be downloading the data no matter what, the question is if you wish to stream it or save it to a file. I don't see any reason not to save it to a local file.
I am assuming that we can use bigBed and bigWig files for making heatmap for those Chip-Seq data in computeMartix. I am new to this if I am wrong please correct me.
You were talking about using data without downloading it. Now you're talking about files. What is your question?
Any application/program you use will need access to data to do its job. You can only access data that is hosted on the internet by downloading it, unless you upload your program to the server the data is on and that way the application can access the data without the data going through a network.
I will download data and perform analysis in a local machine. What are the files needed for heatmap of Chip-Seq data?
I mean, that would be the files containing the data you are using in your heatmap, I guess? Can you specify more details on what you're trying to do? "Create a heatmap out of some data" is all the info available to us right now, and you can create a heatmap out of any matrix of numbers.