Using ChIPpeakAnno on a non-mainstream organism
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 12 months ago
United States
Dear Olivier, As long as you have TSS annotation data with gene ID, chromosome, strand, gene start and end information, you could create a RangedData object, e.g., Tgondii.TSS, which serves as AnnotationData for annotatePeakInBatch function. For detailed information on using anotatePeakInBatch and how to create a AnnotateData object, please type library(ChIPpeakAnno) followed by ?annotatePeakInBatch. To obtain sequences, here is how to forge a BSgenome to be used in ChIPpeakAnno, http://bioconductor.org/packages/2.8/bioc/vignettes/BSge nome/inst/doc/BSgenomeForge.pdf To get enriched GO, you will need org.*.eg.db package for your organism. I think the Bioconductor Core team has built the packages for different organisms using AnnotationDbi. I cced bioconductor listserv to seek input on this. Thanks! Best regards, Julie On 4/24/11 9:20 PM, "Olivier Lucas" <olucas.usf@gmail.com> wrote: Dear Dr Zhu, I have read your paper on ChIPpeakAnno with great interest. I even managed to convinced collaborators that it should be the way to go! I am fairly new to bioconductor as I come from a straight experimental biology background. I am comfortable using R though. I just started a project to study multiple transcription factors in a non-mainstream organism, Toxoplasma gondii (a relative of Plasmodium). I do have a genome available toxodb.org <http: toxodb.org=""> ) with decent annotations, TSS and GO assignments and I am fairly familiar with genomics data (I do a lot of microarrays analysis, mostly using GeneSpring) and how to retrieve pretty much anything from toxodb.org <http: toxodb.org=""> and create BED, GFF etc... I have used Galaxy a bit too. There are no equivalent of Hs.eg.db for Toxoplasma and Toxoplasma is not available through biomaRt. From your ppt, it seems that I could build a mart object for my species even if not in biomaRt? I have looked and practiced ChIPpeakAnno from your online powerpoint from BioC2010. I already have almost 10 ChIP-chip experiment performed (each factor in duplicate at best for now) and data is piling up fast... I am very much looking forward to using ChIPpeakAnno but feel a little bit overwhelmed to the amount of work needed and I am not sure where should I start in term of building the reference data I need and I am not sure what I really need... At this point any recommended workflow for a non-supported organism would help me move forward. Or is this just too daunting of a task? Sincerely, [[alternative HTML version deleted]]
Transcription Annotation GO AnnotationData Organism BSgenome biomaRt BSgenome ChIPpeakAnno • 1.3k views
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