search

YuLab-SMU / ChIPseeker

:dart: ChIP peak Annotation, Comparison and Visualization
https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585
219 stars 74 forks source link

inconsistency with annotatePeak #212

Open fanying2015 opened 1 year ago

fanying2015 commented 1 year ago

Dear GuangChuang,

Thank you for making the convenient and powerful package.

In one example I found inconsistency 'annotation' and mapped gene in the annotatepeak output. In the example attached, the peak was mapped to CAT, but in annotation, it's corresponding to an intron of gene ELF5 (ENST00000257832). When I checked the signal track, mapping to ELF5 makes more sense to me in the example.

I might have missed something. Is there anyway to map the peak to gene based on ['annotation'] column? I'm using the default priority when doing annotation. The package version I'm using is ChIPseeker_1.32.0. The genome annotation is hg38.

Many thanks!

fanying2015 commented 1 year ago

Screen Shot 2022-11-29 at 3 42 53 PM

DengEr-1993 commented 1 year ago

Have you solved this problem ? I also met similar problem and now I am not sure if it is cause only by this package.

I think it is better for you to tell us the session information related to all the packages except ChIPseeker. I also posted my question here yesterday.

Because there are several other packages used during "annotatepeak()". I just check them one by one.

The key is that the version I used is 1.36.0.

It works well if I use old version 1.34.1.

So I think Dr. Yu can give us some help. Here is my new post. https://github.com/YuLab-SMU/ChIPseeker/issues/221

Best, xiangyi