Hi,

I am using ChIPseeker package that you have published to annotate my ChIP-seq data. I am using "annotatePeak" to annotate my peak and make Venn diagram. I have question regarding to genomic annotation that shows in Venn diagram. How do you define 5' UTR, 3' UTR, intergenic region and the end of the genes?

Thank you

5'UTR is extracted by fiveUTRsByTranscript(TXDB) and 3'UTR is extracted by threeUTRsByTranscript(TXDB). These two functions are defined in GenomicFeatures package and the information is already available in TXDB object. ChIPseeker doesn't define them.

For intergenic region, it means the peak doesn't overlap with any genes.

For the end of the gene,  we didn't define it. What we defined that related to the end of the gene is the 'Downstream'. Downstream is the immediate downstream of the gene end. If the peak is located at upstream of the gene end, it is actually inside the gene and will be annotated as overlap with extron or intron.