User: Stefanie

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Stefanie360
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Posts by Stefanie

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processing BamFiles - streaming vs not streaming
... Dear list, I have a question regarding processing of large bamfiles (such as reading in via ‚readGAlignemnts‘ or computing the coverage). I know about the option of iterative processing such as shown in the example below. mybam = open(Bamfile(„bamfile“, yieldSize = 2000000)) gAln <- GAlignmen ...
process written 6.0 years ago by Stefanie360 • updated 6.0 years ago by Michael Lawrence11k
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Comment: C: Computing the coverage on a bamfile with a huge amount of seqlevels
... Its working, thanks! Best, Stefanie Am 28.10.2013 um 19:12 schrieb Hervé Pagès : > Hi Stephanie, > > GenomicRanges 1.14.2 (in BioC release) is available since last Friday. > > In BioC devel though, other problems got in the way but GenomicRanges > 1.15.5 is finally out there (si ...
written 6.1 years ago by Stefanie360
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Comment: C: Computing the coverage on a bamfile with a huge amount of seqlevels
... Here is my SessionInfo, GenomicRanges as well as IRanges should be up-to-date. R Under development (unstable) (2013-10-15 r64056) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY ...
written 6.1 years ago by Stefanie360
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Comment: C: Computing the coverage on a bamfile with a huge amount of seqlevels
... Hi Herv?, I just wanted to try the new coverage function: # I read in a bam file, human data mapped against the transcriptome x = readGAlignments(human_trans_bam) # This is my GAligments object > x GAlignments with 46765032 alignments and 0 metadata columns: se ...
written 6.1 years ago by Stefanie360
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[Fwd: package installation bei Rdevel fails]
... sorry for posting this, wrong addressee! ...
written 6.1 years ago by Stefanie360
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package installation bei Rdevel fails
... Hello Stefan, wenn ich bei meinem Rdevel ein package installieren fkt es schon wieder nicht, keine ahnung warum: [stefanie at ebersberger-46-146 ~]$ Rdevel > source("http://bioconductor.org/biocLite.R") > biocLite("GenomicRanges") ERROR: failed to lock directory ?/home/stefanie/R/x86 ...
written 6.1 years ago by Stefanie360
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Comment: C: Computing the coverage on a bamfile with a huge amount of seqlevels
... Thanks a lot! Can?t wait to try the new version! Best, Stefanie Am 25.10.2013 um 12:44 schrieb Hervé Pagès : > Hi Stephanie, > > Just to let you know that in GenomicRanges 1.14.2, coverage() should > now be much faster on objects with many seqlevels. Should be about > 1000x faster ...
written 6.1 years ago by Stefanie360
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Comment: C: Computing the coverage on a bamfile with a huge amount of seqlevels
... Thanks for the answer! Just wanted to make sure that I don't miss a relevant feature . Best, Stefanie Am 17.10.2013 um 22:07 schrieb Hervé Pagès : > Hi Stephanie, > > On 10/17/2013 07:37 AM, Stefanie Tauber wrote: >> What is the best way to compute the coverage on a ReadGAlignments ...
written 6.1 years ago by Stefanie360
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Computing the coverage on a bamfile with a huge amount of seqlevels
... What is the best way to compute the coverage on a ReadGAlignments object when I have many, many (about 50 000) seqlevels? Just computing coverage(object) is terribly slow due to the huge amount of seqlevels. At the moment, I am subsetting the ReadGAlignments object for each seqlevel, I omit the r ...
coverage written 6.1 years ago by Stefanie360 • updated 6.1 years ago by Hervé Pagès ♦♦ 14k
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Comment: C: coverage on very large ReadGappedAlignmentsObject
... To be more specific, it takes about 10 minutes to calculate the coverage of 1 x 10^6 reads on my pc (linux, 4 cpus, 8GB RAM) This seems a bit long to me, what do you think? Am 08.05.2013 um 17:09 schrieb Steve Lianoglou : > Another approach to what Martin suggests would be to simply read in ...
written 6.5 years ago by Stefanie360

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