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.
1. Yes, “CFDscore” in CRISPRseek is calculated based on the table “NatureBiot2016SuppTable19DoenchRoot" (Doench et al., 2016) and Percent-Active column.
2. CFDscore is calculated using mismatch type and mismatch position although the mismatch activity is given as pos 20, 19, 18,....1 ...
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Thanks for your attention!
... Please take a look at https://www.bioconductor.org/packages/release/bioc/html/dagLogo.html and see if dagLogo fits your needs. Thanks!
On Mar 6, 2018, at 9:58 PM, petyuk [bioc] <email@example.com<mailto:firstname.lastname@example.org>> wrote:
Activity on a post y ...