User: Michael Stadler

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Posts by Michael Stadler

<prev • 31 results • page 1 of 4 • next >
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Answer: A: QuasR: Loading BAM files as start point
... Dear Rahel, Regarding splicedAlignment=TRUE: As you are using external bam files, this parameter will not have any effect on the alignments themselves. It would only matter if you are doing the alignments within QuasR. It's purpose is here to "tell" QuasR that the bam files may contain spliced alig ...
written 2.2 years ago by Michael Stadler310
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Answer: A: QuasR: Loading BAM files as start point
... Dear Rahel, My guess is that you have a problem in the file "sample_file.txt". Make sure that it only contains two columns in each row, separated by a single tab-character. The first error message that you got ("... should only contain the columns names ...") is only thrown when your samples file c ...
written 2.2 years ago by Michael Stadler310
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Answer: A: QuasR question
... Dear Dani, Please have a look at the documentation of qAlign. The sampleFile argument takes the path and filename of a text file, which in turn contains the paths and file names of the sequence or bam files. What you do is to directly pass the bam file name, which is not the same. QuasR comes wit ...
written 3.2 years ago by Michael Stadler310
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QuasR question
... Dear Dani, I hope you don't mind me cc'ing the bioconductor list. The question may be of interest to others. The answer to your questions is described in the vignette (section 5.1 "Create a sample file"). Essentially, you just list the pre-existing bam files instead of the sequence files. QuasR wi ...
quasr written 3.2 years ago by Michael Stadler310 • updated 3.2 years ago by Daniel Soronellas10
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Comment: C: Rbowtie - compilation error
... Thanks Martin for notifying! Michael On 04.06.2014 13:22, Martin Morgan wrote: > Please remember to include the package maintainer in mail about > individual packages. The maintainer is available from the package > 'landing page' > > http://bioconductor.org/packages/release/bioc/ht ...
written 3.5 years ago by Michael Stadler310
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Answer: A: Rbowtie - compilation error
... Hi Romain, Great, thank you very much for testing. I am copying the list again so others who might run into the problem are aware that an update to Rbowtie version 1.4.5 (release) or 1.5.5 (development) should solve the issue. Best wishes, Michael On 05.06.2014 18:06, Romain Retureau wrote: > ...
written 3.5 years ago by Michael Stadler310
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Answer: A: Rbowtie - compilation error
... Hi Romain, Please find my replies below: On 05.06.2014 11:05, Romain Retureau wrote: > Hi, > > here is the output of uname -a : > > /"Linux retureau-MacBookPro 3.2.0-63-generic-pae #95-Ubuntu SMP Thu May > 15 23:26:11 UTC 2014 i686 i686 i386 GNU/Linux//"/ > / > / > I did ...
written 3.5 years ago by Michael Stadler310
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Answer: A: Rbowtie - compilation error
... Dear Romain, Thank you for the report. I am also using Ubuntu 12.04 LTS, and cannot reproduce your issue, however I am using 64-bit R, while you are using a 32-bit version. Could you test the following things to narrow down the problem: 1. what is the output of: uname -a 2. can you compile bowti ...
written 3.5 years ago by Michael Stadler310
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QuasR for miRNA
... Dear Simon, I hope you don't mind that I am copying the Bioconductor list - your question may be relevant to others as well. The reason for extending the mature miRNA coordinates depending on their strand lies in the way QuasR's qCount determines if an alignment overlaps with a query region: By d ...
mirna quasr written 3.5 years ago by Michael Stadler310
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Comment: C: QuasR: problem accessing BSgenome.Rnorvegicus.UCSC.rn5
... Hi Guido and Herve, You were both spot on. In the development version 1.3.9 of QuasR, we adapted to the new (BioC 2.14) type of BSgenome packages, so QuasR >= 1.3.9 only works with these. One clarification regarding the treatment of masks in QuasR: - QuasR <= 1.2.x has ignored masks in BSge ...
written 3.7 years ago by Michael Stadler310

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