User: 94133

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941330
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Posts by 94133

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Comment: C: ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
... That works, thanks!  ...
written 13 months ago by 941330
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Comment: C: ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
... I tried your suggestion like this but get an error: ChIP_peaks_annoTSS <- annotatePeakInBatch(res1_ChIP,                                             AnnotationData = genes(TxDb.Mmusculus.UCSC.mm10.knownGene),                                             output = "overlapping",                   ...
written 13 months ago by 941330
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Comment: C: ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
... No. Are you suggesting this is the best way to do this? I don't understand why one would use upstream for TSS overlap, can you explain? Thanks! ...
written 13 months ago by 941330
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ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
... I want ChIP peaks that overlap gene TSSs. However, output from ChIPpeakAnno returns peaks that do not overlap, which requires extra filtering. Is there a better way? ChIP_peaks_annoTSS <- annotatePeakInBatch(res1_ChIP,                                             AnnotationData = genes(TxDb.Mmusc ...
chipseq chippeakanno R written 13 months ago by 941330 • updated 13 months ago by Ou, Jianhong1.1k
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Comment: C: ChIP peak annotation: how to get all genes that overlap each peak?
... Great, thanks for your quick reply! ...
written 15 months ago by 941330
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Comment: C: ChIP peak annotation: how to get all genes that overlap each peak?
... Thanks! Is there a way to keep res as "GRanges" object?   ...
written 15 months ago by 941330
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Comment: C: ChIP peak annotation: how to get all genes that overlap each peak?
... Thanks for your reply! I tried that but get: Error in as.vector(x) : no method for coercing this S4 class to a vector Suggestions? I made workaround with dplyr, but have to convert from class "GRanges" to "data.frame" to do that.       ...
written 15 months ago by 941330
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ChIP peak annotation: how to get all genes that overlap each peak?
... How do I get all genes that overlap a peak as a comma separated column within a single row for the peak? I tried ChIPseeker: annotatePeak(peaks, level = "gene",                           addFlankGeneInfo = FALSE,                          assignGenomicAnnotation = TRUE,                          TxD ...
chippeakanno chipseeker chip-seq written 15 months ago by 941330
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Comment: C: CSAW Spike In Normalization: Error in .local(object, ...) : library sizes of
... Do you have a suggested workflow for aligning to combined genomes? I agree with the points that you raised here, thanks for your input! The primary advantage of spike-in normalization is to draw empirical quantitative normalization between control and treated samples, especially in cases where ther ...
written 17 months ago by 941330
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Comment: C: CSAW Spike In Normalization: Error in .local(object, ...) : library sizes of
... Thank you for your help! Wouldn't aligning to a combined human/mouse reference (presumably by changing chrom names, i.e. mchr1 v hchr1) suffer from the same putative double mapping issue? Alternatively, one could throw out reads that map to both genomes, but this seems like a very bad idea because ...
written 17 months ago by 941330

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