Hi, I'm new to R and struggling to follow the guide for ATACseqTFEA found here . The guide's example is for the Drerio genome chromosome 1, in a limited Granges to scan for binding sites.
However, for my full experiment, I want to scan the whole mouse genome. My problem is that the code I'm running for this purpose takes forever to run (so far has taken ~24 hours and currently still running). Is that very normal for this type of analysis? I understand I'm working with big data, but does a more efficient solution exist? Below is the code I entered. I omitted the arguments specifying chromosome/Granges within the genome in order to include the whole thing.
library(ATACseqTFEA) library(ATACseqQC) library(BSgenome.Mmusculus.UCSC.mm10) motifs <- readRDS(system.file("extdata", "PWMatrixList.rds", package="ATACseqTFEA")) bindingSites <- prepareBindingSites(motifs, Mmusculus, p.cutoff = 5e-05)
Any guidance would be much appreciated.