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/BSgenome/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,

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