How to create GRanges for TES
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@marpieraccioli-23381
Last seen 8 months ago
Italy

Hi, I'm interested in analyzing average density of reads from CLIP-seq experiments in the 3'UTR and around TES (transcription end site) of genes. For ChIP-seq analysis, the promoters function of "GenomicFeatures" package computes a GRanges object that spans the promoter region around the transcription start site for the transcripts in a TxDb object.Subsequent upstream 0and downstream arguments define the number of bases upstream and downstream from the transcription start site that make up the promoter region. How to create a GRanges object that spans region around TES (transcription end site) of the genes? Thank you, Marco

GenomicFeatures TxDb CLIP-Seq • 310 views
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@michael-lawrence-3846
Last seen 5 months ago
United States

I guess you could invert the strand and use promoters(). Another option is flank(gr, width, both=TRUE, start=FALSE) but note that the width is divided equally upstream and downstream (it's symmetric).

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Thank you so much for your quick reply! I tried creating a GRanges object with a list of hg19 TES ( +/- x base pairs upstream/downstream of TES position). Is it a good solution?