What if I have only one replicate per condition, and is there any way to ignore the QC?

[sameet]

I have the following:

'''
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 = 1,
                                                                     primary_enz = "CATG",
                                                                     samples = c("Re", "Ri"),
                                                                     conditions = c("Reference", "Risk"),
                                                                     species = "hs",
                                                                     output_dir = "./bait_1A_results"
                                                                      enz_file = enz.df)

Error in createR4CkerObjectFromFiles(files = fl, bait_chr = "chr12", bait_coord = 125313518,  : rence" Number of samples does not matchdir = "bait1A_results", enz_file = enz.df)
"""

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.

[rr1859]

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)

[sameet]

Ah,

That is useful. Thanks.

Sameet