AnnotatePeakInBatch in the ChIPpeakAnno package should do.
The following parameters need to be reset.
BSgenomeName = Mmusculus, chromToSearch = "all"
On Jul 29, 2018, at 7:37 PM, jacob.bradford [bioc] <email@example.com<mailto:firstname.lastname@example.org>> wrote:
Activity on a post you are following on supp ...
Score is required here. The following example should run fine.
which <- GRanges(seqnames = "chr1", ranges = IRanges(seq(10000, 2000000, by=1000), width = 100), score = rep(1,1991))
seqlengths(which) = 248956422
bamfile <- system.file("extdata", "GL1.bam",
Thanks for the feedback!
Regarding the output from cumulativePercentage, you are unlikely to get a plot that looks exactly the same as the one shown in the vignette. The further away from the y = x line the curve is, the higher the signal noise ratio is.
We will add the Transcription Start ...
Thanks for the detailed description of the problem and the session information!
What happened is that the mutated gRNA does not have a perfect matched target site on chromosome X. The error occurred because you were trying to search for RE sites on the flanking regions of a non-extent gen ...
Your understanding of all the columns is correct except uniqueREin200, which contains the unique restriction enzyme names in upstream 100 and downstream 100 around the gRNA.