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how to normalize tag count to 10 million reads without using homer?

Hi, I know homer can normalize tag count to 10 million reads but do you know any other methods to do the normalize part except using homer? like macs2 itself, or .... Thanks,

chip-seq normalize
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updated by ATpoint ATpoint • written by mikysyc2016 mikysyc2016

1 answer

Again, like in your previous questions, if you ask for a solution, you have to specify what kind of input data you have. Please keep that in mind for the future. If you have a count matrix, you can do it with a one-liner in R:

matrix_norm10mio <- data.frame(round(sweep(matrix_raw_counts, 2, colSums(matrix_raw_counts), FUN = "/") * 10000000))

You can scale to any number of reads by replaceing the 10.000.000 at the end by the intended number of total reads. This is of course a very simple way of normalizing counts.

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written by ATpoint ATpoint

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