User: manuel.goepferich

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Posts by manuel.goepferich

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Comment: C: Peaks in coverageByTranscript {GenomicFeatures}
... What I did was something like this (and now it looks similar to me coverage vectors): plot(decode(tx_cvg$FBtr0308296)) The story goes as follows: My supervisor asked me where this wiggly shapes of coverage vectors are coming from? I see that with 'runmean' the coverage vectors will be smoothed. ...
written 7 months ago by manuel.goepferich0
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Comment: C: Peaks in coverageByTranscript {GenomicFeatures}
... Thanks. It is definitely part of the answer. I have checked the explanations & the help pages. I will give an example for a decoded coverage vector (paired-end reads, star-mapping, mouse-genome, single cell, start of a 3'UTR): 62 62 62 59 53 53 53 53 52 50 50 50 50 45 45 45 45 45 42 42 42 43 4 ...
written 7 months ago by manuel.goepferich0
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Peaks in coverageByTranscript {GenomicFeatures}
... Hi, for my project it would be very important to know how the function coverageByTranscript {GenomicFeatures} really works. For many coverage plots (coverage of a 3'UTR) I get no step functions but rather spikes. Is the whole read considered as coverage or just the end or start (How many base p ...
genomicfeatures written 7 months ago by manuel.goepferich0 • updated 7 months ago by Hervé Pagès ♦♦ 13k

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