Question: chipseeker annotation of focused genic regions
0
gravatar for wuzefeng2008
2.1 years ago by
wuzefeng20080 wrote:

I am attempting to annotate some ChIP-Seq data that I have called using MACS2. I just want to annotation peaks to specific regions, such as following classes : promoter, 5’ untranslated region (UTR), 3’ UTR, coding exon and intron),and intergenic regions from gtf file( convert to 'TxDB'). However,  the result always output annotations  to regions which i do not care about, like first intron, first exon and downtream 3000. How to set my focused regions?

chipseeker annotatepeak • 424 views
ADD COMMENTlink modified 2.1 years ago by Guangchuang Yu1.1k • written 2.1 years ago by wuzefeng20080
Answer: chipseeker annotation of focused genic regions
2
gravatar for Guangchuang Yu
2.1 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

first exon belongs to exon.

first intron belongs to intron.

downstream belongs to intergenic.

You can simply convert 1st exton to exon etc.

ADD COMMENTlink written 2.1 years ago by Guangchuang Yu1.1k
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