User: sarac

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sarac20
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Posts by sarac

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Comment: C: Behaviour of getCTSS on a CAGEset - extra reads?
... Thank you for your reply and for advice on the work around. ...
written 12 weeks ago by sarac20
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Comment: C: Genome database and transcription database have different lengths
... Thank you! Number 1 worked a treat. ...
written 12 weeks ago by sarac20
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Comment: C: Behaviour of getCTSS on a CAGEset - extra reads?
... Hi Charles, Many thanks for getting back to me. When I output the ctss object above as a table I get, for example, the following: chr5 150412750 - 2 chr5 150412751 + 9932 chr5 150412751 - 48 chr5 150412752 + 514 chr5 150412752 - 235 chr5 150412753 + 261 chr5 150412753 - ...
written 12 weeks ago by sarac20
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Genome database and transcription database have different lengths
... While trying to assign transcript IDs to my tags using the `CAGEfightR` package: TSSs <- assignTxID(TSSs, txModels = txdb, swap="thick") I was met with the following error: Error: seqlengths(object) not identical to seqlengths(txModels) Unless I am mistaken, this seems to arise becaus ...
cage cagefightr written 12 weeks ago by sarac20 • updated 12 weeks ago by maltethodberg130
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Behaviour of getCTSS on a CAGEset - extra reads?
... When counting reads from a bamfile, I manually extracted the reads aligned to a particular location and found that CAGEr had clustered some reads at the location that did not exist in the bamfile. The commands I am using are: > My_CAGEset <- new("CAGEset", genomeName = "BSgenome.Hsapien ...
cager cage ctss written 3 months ago by sarac20 • updated 12 weeks ago by Charles Plessy110

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