Hello all,
I've been trying a package called 'MEDIPS' for MeDIP-seq analysis for few days now. The manual says : The genome will be divided into adjacent windows of length 100nt and all further calculations (short read coverage,
differential coverage between conditions etc.) will be applied to these windows, if ws =100. I've seen a paper (PMC4213696) apart from MEDIPS's original paper that researchers are using ws = 100 only.
My question is what is the criteria for selecting window size? What if I increase the window size ? I guess the values such as 'counts', 'logFC' , 'rpkm' & eventually 'p-value' will change, is I do so.
Please help me out.
Thank you :)
package : https://www.bioconductor.org/packages/release/bioc/html/MEDIPS.html