Search
Question: chipseeker annotation of focused genic regions
0
gravatar for wuzefeng2008
8 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 8 months ago by Guangchuang Yu1.0k • written 8 months ago by wuzefeng20080
2
gravatar for Guangchuang Yu
8 months ago by
Guangchuang Yu1.0k
Hong Kong
Guangchuang Yu1.0k 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 8 months ago by Guangchuang Yu1.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 300 users visited in the last hour