ChIPseeker annotation
I have annotated my bed peak file using ChIPseeker R package (annotatepeak function). All the peaks lying within -3000 bp to +3000 bp from the TSS are annotated to the gene of that TSS. But I want to calculate the percentage of overlap of the peak to the TSS region. Is there a way to calculate it? Is it possible that peak may be located far off from the gene but still lying within the TSS region?
• 871 views
•
link
updated
by
Nitin Narwade
•
written
by
sk_24 •
•
written
by
sk_24 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
should I remove the transcripts from annotate peak region in ATAC-seq
written by QX •
-
annotatePeak error for some problem
written by Jones •
-
best annotation approach for peaks
written by Chironex •
-
Why not use ONLY promoter-bound peaks when testing for enrichment in differentially-bound regions?
written by e.r.zakiev •
-
Question about ChIPseeker parameters
written by Jen •
-
Help generating multiple annotations under one H3K27me3 peak
written by Rory Osborne •
-
Changing distance to TSS (tssRegion in ChIPseeker) during peak annotation in ChIP-seq analysis does…
written by vyazar •
-
ChIPseeker missing full annotation
written by rbronste
-
Chipseq peak analysis using ChIPseeker
written by Mike
-
Tool: ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization
written by Guangchuang Yu
I think you can use ChIPpeakAnno for this.
Regards,
Nitin N.