why are all DiffBind tutorial’s ATAC-seq peak intervals 400 bp for all intervals?
I have followed DiffBind tutorial 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.
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See section 3.3. in the manual:
(…) As this example is based on a transcription factor that binds to
the DNA, resulting in “punctate”, relatively narrow peaks, the default
option to re-center each peak around the point of greatest enrichment
is appropriate. This keeps the peaks at a consistent width (in this
case, the default summits=200 results in 401bp-wide intervals,
extending 200bp up- and downstream of the summit)
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