Question: chipseeker annotation of focused genic regions
gravatar for wuzefeng2008
5 months 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?

ADD COMMENTlink modified 5 months ago by Guangchuang Yu960 • written 5 months ago by wuzefeng20080
gravatar for Guangchuang Yu
5 months ago by
Hong Kong
Guangchuang Yu960 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 5 months ago by Guangchuang Yu960
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