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Unclear Peak Annotation

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 IGV-snapshot of an annotated peak .

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

chipseeker annotation
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written by laura.mannarino • 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

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written by laura.mannarino • laura.mannarino

1 answer

but CLSTN2 has got 17 exons, not 10

10 is intron

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written by Guangchuang Yu Guangchuang Yu

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?

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written by laura.mannarino • laura.mannarino

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