Hi,

I am analyzing mandarin duck (Aix galericulata) ChIP-Seq data. We have a mandarin duck genome assembly .fa file and a genome annotation .gff file produced by our cooperators. May I know whether ChIPQC can analyze mandarin duck histone modification ChIP-Seq data? Could you show me how to do it, if it is doable? Many thanks.

Best,

Gary

hi Gary,

ChIPQC should work fine for BAM files aligned to any genome. Since there isn't a prebuilt TxDB package for mandarin duck, the summary of gene signal within genic regions is not immediately supported.

To run ChIPQC on a single BAM.

ChIPQCsample("MyDuckData.bam")

I would recommend running all your samples together using the ChIPQC function with a sample sheet showing the set-up of your experiment. This is detailed in the package vignette (http://bioconductor.org/packages/release/bioc/vignettes/ChIPQC/inst/doc/ChIPQC.pdf)

You can also  provide custom annotation to ChIPQC in the form of a list of GRanges objects. This is described in this workshop

http://bioconductor.org/help/course-materials/2014/BioC2014/Bioc2014_ChIPQC_Practical.pdf

and in this previous post

creating custom genome annotation for the ChIPQC package

If you have a gtf for gene models you should be able to build a ChIPQC annotation for your genome of interest.

require(GenomicFeatures)
require(GenomicRanges)

txdb <- makeTxDbFromGFF("MyGTF.gtf",format="gtf") 

All5utrs <- reduce(unique(unlist(fiveUTRsByTranscript(txdb))))
All3utrs <- reduce(unique(unlist(threeUTRsByTranscript(txdb))))
Allcds <- reduce(unique(unlist(cdsBy(txdb,"tx"))))
Allintrons <- reduce(unique(unlist(intronsByTranscript(txdb))))
Alltranscripts <- reduce(unique(unlist(transcripts(txdb))))

posAllTranscripts <- Alltranscripts[strand(Alltranscripts) == "+"]
posAllTranscripts <- posAllTranscripts[!(start(posAllTranscripts)-20000 < 0)]
negAllTranscripts <- Alltranscripts[strand(Alltranscripts) == "-"]
chrLimits <- seqlengths(negAllTranscripts)[as.character(seqnames(negAllTranscripts))]      
negAllTranscripts <- negAllTranscripts[!(end(negAllTranscripts)+20000 > chrLimits)]      
Alltranscripts <- c(posAllTranscripts,negAllTranscripts)
Promoters500 <-  reduce(flank(Alltranscripts,500))    
Promoters2000to500 <-  reduce(flank(Promoters500,1500))
LongPromoter20000to2000  <- reduce(flank(Promoters2000to500,18000))

duckAnnotation <- list(version="",LongPromoter20000to2000=LongPromoter20000to2000,
            Promoters2000to500=Promoters2000to500,Promoters500=Promoters500,
            All5utrs=All5utrs,Alltranscripts=Alltranscripts,Allcds=Allcds,
            Allintrons=Allintrons,All3utrs=All3utrs)

ChIPQCsample("MyDuckData.bam",annotation=duckAnnotation)

very best,

tom