Question: mm9 genomic annotation UTR, Codon, Promoter
gravatar for kanwarjag
5.7 years ago by
United States
kanwarjag1.0k wrote:

I have a CLIP-seq data and would like to overlay with various genomic features like UTRs, Exons, introns, promoters etc. from mm9 I have looked at the following posts-

Where To Download Genome Annotation Including Exon, Intron, Utr, Intergenic Information

Define If Chip Peaks Are Located In Exon, Intron, Promoter, 3Prime Utr

ut could not figure out how in  we can extract such features in one file. Is there any source which may have such GTF/ GFF3 file or any suggestion how I can extract such file with all features  from UCSC, biomart or Ensemble


Thanks for any pointer/s


intron exons 5'utr promoter 3'utr • 2.3k views
ADD COMMENTlink modified 4.6 years ago by cooleel0 • written 5.7 years ago by kanwarjag1.0k
gravatar for A. Domingues
5.7 years ago by
A. Domingues2.3k
Dresden, Germany
A. Domingues2.3k wrote:

For ChIP-seq I use the bioconductor package ChIPseeker and the function `annotatePeak`. I see no reason why it would not work also for CLIP-seq data, in essence a set of genomic features just like chip-seq peaks. I really like how easy it is to visualize the comparison of multiple datasets, and you can input your own annotation.

ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by A. Domingues2.3k
gravatar for marina.v.yurieva
5.7 years ago by
Farmington, CT
marina.v.yurieva520 wrote:
Google suggests something called PIPE-CLIP specifically for CLIP-seq data. I use Homer to annotate ChIP-seq.
ADD COMMENTlink written 5.7 years ago by marina.v.yurieva520
gravatar for cooleel
4.6 years ago by
cooleel0 wrote:

Do you use PIPE-CLIP now?

anyone knows what happened on that program?  I got an error on Galaxy site of PIPE-CLIP.

and when I was running it locally, on ubuntu environment I also got error. always can not go through the whole process of that program.


Any suggestions appreciated. Thanks!


ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by cooleel0
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