I have followed DiffBind tutorial https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf I have found out that the returned count matrix's peak intervals are always 400bp. Literally, all the peak intervals in the count matrix are 400 bp. I am wondering why it is happening.
this was the case for my own data as well.
My code is as follows.
library(DiffBind) samples <- read.csv("tamoxifen.csv") DBdata1 <- dba(sampleSheet=samples) DBA <- dba.count(DBdata1,score=DBA_SCORE_READS) counts <- dba.peakset(DBA, bRetrieve=T, DataType=DBA_DATA_FRAME)
when I inspect the count matrix returned in the above code, it looks like the following
CHR START END BT4741 ... chr18 90841 91241 2 chr18 111395 111795 21
If you subtract END from START, you will get 400bp. The answer is the same for the entire dataset.