mm9 genomic annotation UTR, Codon, Promoter

Question

[kanwarjag]

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

but 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 Ensembl

Thanks for any pointer(s)

Answer 1

[A. Domingues]

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.

Answer 2

[marina.v.yurieva]

Google suggests something called PIPE-CLIP specifically for CLIP-seq data. I use Homer to annotate ChIP-seq.

[cooleel]

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!