CHIP Seq Analysis by DiffBind Package

Question

[shrinka.genetics]

Hi I am working on ChipSeq data of histone marks. I am using Diffbind package. I have 8 samples in 2 groups each. I am trying to see differential peak enrichment in these two groups. I have used this to read one file at a time. How can I club 4 samples so that I can do a group comparison?

bedJ <- as.data.frame(read.table("CEMT_178.H3K27ac-J.bed",header = FALSE, sep="\t",stringsAsFactors=FALSE, quote=""))

Thanks Shrinka

[ATpoint]

What is unclear after reading the manual, especially section 3? https://www.bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf

Answer 1

[Rory Stark]

The easiest way to get these data into DiffBind is to to use a sample sheet with entries for the aligned reads, peaks, and other metadata for each sample.