Question: After Annotation in R , the binding sites are less than the starting downloaded from ENCODE Chip-seq Matrix
gravatar for atsalaki
2.6 years ago by
atsalaki10 wrote:

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?

chip-seq peaks • 732 views
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