Closed sameet closed 7 years ago
Hi,
You have to specify the number of replicates per sample.
enz.df <- read.table("hg19_nlaiii_flanking_sites_76_unique_2.bed", stringsAsFactors = F) fl <- list.files("bait1A", pattern = "*und.bedGraph", full.names=T) my_obj <- createR4CkerObjectFromFiles(files = fl, bait_chr = "chr12", bait_coord=125313518, bait_name="1A", replicates = c(1,1) primary_enz = "CATG", samples = c("Re", "Ri"), conditions = c("Reference", "Risk"), species = "hs", output_dir = "./bait_1A_results" enz_file = enz.df)
Ah,
That is useful. Thanks.
Sameet
I have the following:
Is there anyway this calculation could be wrong. When I do the following, I am pretty sure it should pass the QC. More than 40% of the reads are within 1 kB of the bait location. Any help will be greatly appreciated.