After Annotation in R , the binding sites are less than the starting downloaded from ENCODE Chip-seq Matrix · Biostar

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After Annotation in R , the binding sites are less than the starting downloaded from ENCODE Chip-seq Matrix

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

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updated 5.9 years ago by Biostar

• written 9.9 years ago by atsalaki •

Can you provide the results of the following code:

str(gr_narrowPeak)
str(annotatePeakInBatch(gr_narrowPeak, featureType = c("TSS"),maxgap=5000 ,AnnotationData=annotationData , output="overlapping", FeatureLocForDistance="TSS") ))

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written 5.9 years ago by Friederike

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