User: loretta

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loretta0
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Posts by loretta

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Handing duplicates in DiffBind
... Hi Rory, I had been previously, not marking duplicates or removing them in my ChIP-Seq datasets, and instead setting the dba.count bRemoveDuplicates to TRUE. Firstly, how adverse is this strategy when determining differential peaks? And secondly, how does setting bUseSummarizeOverlaps to TRUEcompa ...
diffbind dba.count bremoveduplicates busesummarizeoverlaps written 8 months ago by loretta0 • updated 8 months ago by Rory Stark2.9k
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Comment: C: DiffBind: Error in heights * sapply(called, function(x) x)
...  Hi Rory,  I received the same error with dba.count() called with summits=25, it also seems to require significantly more memory.  > DBA.count = dba.count(DBA, score = DBA_DESEQ2, bUseSummarizeOverlaps = FALSE, mapQCth = 30, bCorPlot = TRUE, bParallel = TRUE, minOverlap = 2, summits = 25, bRemo ...
written 11 months ago by loretta0
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Comment: C: dba.count Can't count: some peaksets are not associated with a .bam file.
... Thank you Rory. Seems it was just the file path that had an error. ...
written 11 months ago by loretta0
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dba.count Can't count: some peaksets are not associated with a .bam file.
... Hi,  I am having some trouble with the dba.count function in Diffbind dba.count function. See below:  DBA.count = dba.count(DBA, bUseSummarizeOverlaps = FALSE, mapQCth = 30, bCorPlot = FALSE, bParallel = TRUE, minOverlap = 2) Error in pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, default ...
diffbind written 12 months ago by loretta0 • updated 12 months ago by Rory Stark2.9k

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