Question: Unclear Peak Annotation
0
gravatar for laura.mannarino
2.1 years ago by
laura.mannarino0 wrote:

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 • 560 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by laura.mannarino0

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

ADD REPLYlink written 2.1 years ago by laura.mannarino0
0
gravatar for Guangchuang Yu
2.1 years ago by
Guangchuang Yu2.3k
China/Guangzhou/Southern Medical University
Guangchuang Yu2.3k wrote:

but CLSTN2 has got 17 exons, not 10

10 is intron

ADD COMMENTlink written 2.1 years ago by Guangchuang Yu2.3k

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?

ADD REPLYlink written 2.0 years ago by laura.mannarino0
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