User: guillaume.dachy

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Posts by guillaume.dachy

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Trouble while concatenating VRanges object ()
... Dear Julian,  Thank you so much for taking the time to answer my questions. To answer yours : The VCFs are not very different when I look at them, but indeed the error is reproduced when I try to combine VCFs from different experiments (but same sequencer, same tumor, same genes analyzed, same ...
written 10 weeks ago by guillaume.dachy0
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Trouble while concatenating VRanges object ()
... Hi everyone,  I am using the very interesting SomaticSignatures package, and I have an Error now for which I didn't manage to find an answer on this support site.  I managed to concatenate some VRanges objects to one, and so all the functions are working wonderfully to get some signatures, but for ...
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Answer: A: SomaticSignatures package : motifMatrix function trouble
... Sorry for the late response, thank you so much ! I am going to try to have a better annotated matrix.  Cheers ...
written 3 months ago by guillaume.dachy0
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SomaticSignatures package : motifMatrix function trouble
... Hello everyone,  I am trying to use the SomaticSignatures package, which have a very complete vignette but I encounter trouble with the motifMatrix function.  I built a vr object with my reference genome and a VCF file. Then I get a "VRanges object with 6 ranges and 70 metadata columns" and from t ...
somaticsignatures written 5 months ago by guillaume.dachy0
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RNA Seq // QuasR : Error while extracting unmapped reads
... Hi everyone, I'm trying to use QuasR since weeks now for his precious function allowing to align an auxiliary genome, but I get some trouble which are maybe very naive ... but hard to resolve for me !  Does this following error message does an idea to someone ?  > file.copy(system.file(packag ...
rnaseq quasr quasr error paired-end reads written 10 months ago by guillaume.dachy0
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Error in qAlign, QuasR, in paired-end RNA Seq
... Hello ! I'm trying to use QuasR but I have a new error message using qAlign : The early beginning goes well, and then I get this : (I use as genome "BSgenome.Hsapiens.UCSC.hg19" and a auxiliary genome) Available cores: nodeNames ae1.jbd 1 Performing genomic alignments for 2 samples. See pr ...
rnaseq quasr paired-end reads written 10 months ago by guillaume.dachy0
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Error preprocessReads : Error in writeFastq
... Hello everyone ! I'm trying to preprocess paired-end reads in the QuasR Package, but I unfortunately get this error, which is surprising for me because that code worked on windows but not on linux (fedora).  This could be a very naive question, and I apologize if it is... But thank you so much for ...
rnaseq quasr paired-end reads written 11 months ago by guillaume.dachy0
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Comment: A: How to isolate gene from a single chromosome, RNA Seq experiment, using R packag
... Dead Hans-Rudolf,  Thank you for your quick answer !  my problem is the following : my reference genome (GTF) does not contain any information on my transgene, which is referenced as an extra chromosome. (the experiment was a transfection of a human gene in a mouse cell line) My question is then ...
written 11 months ago by guillaume.dachy0
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How to isolate gene from a single chromosome, RNA Seq experiment, using R package ?
... Hi everyone  In a RNA Seq experiment where we put a transgene in mice cells, my gene of interest (that transgene) is on an "artificial" chromosome which contains only this gene. I'm trying desesperately to isolate that chromosome from the data, using R package cummeRbund (DESeq2 and edgeR are optio ...
rnaseq cummerbund R written 11 months ago by guillaume.dachy0 • updated 11 months ago by Gordon Smyth32k

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