Unclear Peak Annotation

Question

[laura.mannarino]

Hi, I have used ChIPseeker to annotate ChIP-Seq peaks and I have found some cases that I don't know how to interpret. I reported here an example of .

The peak that you see in the figure in red (biostar_ex.bed ) is annotated to TRIM42 gene, and actually you can see it upstream of this gene. However, its annotation is Intron (uc003etm.2/64084, intron 8 of 10), and I think it is just because it is on the intron 8 of CLSTN2 gene, but CLSTN2 has got 17 exons, not 10. Therefore, I don't know how to interpret this result. Can you help me, please?

Thanks Laura

[laura.mannarino]

Yes, I am sorry, I wanted to say 16 introns, so I would have expected uc003etm.2/64084, intron 8 of 16 and not uc003etm.2/64084, intron 8 of 10. Does it make sense or am I misunderstanding the annotation?

Thanks

Answer 1

[Guangchuang Yu]

but CLSTN2 has got 17 exons, not 10

10 is intron

[laura.mannarino]

Yes, I am sorry, I wanted to say 16 introns, so I would have expected uc003etm.2/64084, intron 8 of 16 and not uc003etm.2/64084, intron 8 of 10. Does it make sense or am I misunderstanding the annotation?