I am very new to ChipSeq and am just so confused. I have my sequence data, the control and the reference from NiH and UCSC. I have successfully (I think) , mapped the reference, aligned them with bowtie and found peaks with MACS2. The output of MACS2 was a .r file, a .xls file, a .narrowPeak file and a .bed file. I now want to move onto finding differentials. Everything I read watch tells me I need a sample sheet. Is this the .xls file? Or do I need to create something else? Right now this is my R script:
library(ChIPQC) library(DiffBind) library(tidyverse) sampleSheet <- read.csv("meta/peaks.xls") db <- dba(sampleSheet =sampleSheet)
When I look at the created object the output is:
15741 Samples, 0 sites in matrix
Obviously I'm doing something wrong. Any help would be greatly appreciated.