Dear bioc-sig-sequencing,
I would like to prepare a display in a browser like that in the 'PeakSeq' paper
(nat. biotech. 27 66-75 2009, fig 1a, a ChIP-seq signal profile map).
I would like to start by reading into an R session two Eland aligned data files
to be compared, one the 'treatment', and one the input control (chipseq
experiment). For example, for 'trt',
ctcf <- readAligned(cerudataDir, pattern, type="SolexaExport", + filter=filt)
Now, how to proceed to my goal in the 1st paragraph?
Perhaps, as in Bioconductor wkshop handout (11/19/09, Seattle), 'A ChIP-Seq
Data Analysis',
library(BSgenome.Mmusculus.UCSC.mm9)
mouse.chromlens <- seqlengths(Mmusculus)
cov.ctcf <- coverage(ctcf, width = mouse.chromlens, extend = 126L)
yielding a SimpleRleList structure, or
cov.ctcf$chr10
yielding an Rle structure
Then, perhaps could generate a bed ('bedGraph') (per chromosome) file with four
columns: chromosome, start, end, and score (here the scores are the read depths
above each nucleotide). To save space in the bedGraph file, each 'run' of
nucleotides from the Rle structure might appear in one record?
Can someone suggest if this is an appropriate approach, and if so, how to carry
it through to a bed (bedGraph) file? Or if ill-advised, suggest an alternative?
Thanks,
[email protected]
P. Terry
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