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User: Diana

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Diana10
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Posts by Diana

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Comment: C: Memory issues in summarizeOverlaps funtion
... Really? So simply running se will actually count all reads? That would be great... But how is it possible that tail(assay(se)) gives 9997 as last row and rowRanges(se) gives an object of length 25892? I am sorry for asking these probably basic questions... ...
written 10 days ago by Diana10
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Comment: C: Memory issues in summarizeOverlaps funtion
... Hi, I have still one question about the reduceByYield argument. I have the following code: > csvfile <- file.path("W29-1-1.csv") > sampleTable <- read.csv(csvfile,row.names=1) > sampleTable File 1 W29-1-1-B 2 W29-1-1-F > setwd("C:/Program Files/ ...
written 10 days ago by Diana10 • updated 10 days ago by James W. MacDonald49k
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Comment: C: Memory issues in summarizeOverlaps funtion
... Sorry, currently I am reading in one file. As for the yieldSize argument, I know it exists. I haven't yet tried it, as I assumed it would take a looong time to read the whole file in seperate chunks. I will try it with a yieldSize of 2000000 to start with. ...
written 14 days ago by Diana10
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Comment: C: Memory issues in summarizeOverlaps funtion
... Hi James, Thanks for your answer! Yes, I am reading BAM files. I know the yieldSize argument, but the file itself is about 500 MB, so isn't the memory error a bit strange? What could be an explanation besides low RAM memory (which is not the case)? ...
written 14 days ago by Diana10
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Memory issues in summarizeOverlaps funtion
... Hi all, I get a memory error ('error: cannot allocate vector of size 344.5 Mb') when running summarizeOverlaps in the Genomic alignments package. I have 4 GB RAM (with about 3.8 GB free space) and I use 64 bits R. I also increased the memory.limit size to 3500 and I tried -- vanilla as well. Noth ...
summarizeoverlaps memory written 14 days ago by Diana10 • updated 14 days ago by James W. MacDonald49k
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Splicing large bam file with Rsamtools
... Dear all, I tried to open a bam file with the following script: library(Rsamtools) bam<-scanBam("~/Bamfiles Ivy/W9.1.1.bam") As a result, a memory error occured: Error in value[[3L]](cond) : 'Realloc' could not re-allocate memory (209715200 bytes) file: C:/Users/Dia ...
rsamtools written 19 days ago by Diana10 • updated 19 days ago by Martin Morgan ♦♦ 22k
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RSubread in cygwin
... Hi, I am trying to download the Rsubread package through cygwin, but I can't find Subread in the packages offered in cygwin. Is there any other way to download Rsubread on my windows based computer? Thanks in advance! ...
subread written 5 weeks ago by Diana10

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