Entering edit mode
7.5 years ago
atsalaki
▴
20
I download ENCODE chip-seq broadpeak files and annotate them in R with annotatePeakInBatch(gr_narrowPeak, featureType = c("TSS"),maxgap=5000 ,AnnotationData=annotationData , output="overlapping", FeatureLocForDistance="TSS") .The binding sites i get are less that the starting in the ENCODE peak files (e.g i had 40.000 and after the annotation i get only 14.000 ). Can anyone explain to me why this is happening?
Can you provide the results of the following code: