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:
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)
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.
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A. Domingues
Google suggests something called PIPE-CLIP specifically for CLIP-seq data. I use Homer to annotate ChIP-seq.
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marina.v.yurieva
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!
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