User: markus.riester

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Posts by markus.riester

<prev • 30 results • page 1 of 3 • next >
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Comment: C: errors in version 1.7.53
... Sorry to hear that. Negative counts shouldn't happen, it could be an integer overflow. We can debug offline via email (markus.riester at novartis com). If you can send me an example coverage file (loess normalized) plus the gc.gene.file, that would be great. If this is from a custom panel you don't ...
written 5 weeks ago by markus.riester20
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Comment: C: errors in version 1.7.53
... Hi, I didn't increase in the version number because 1.7.55 wasn't build yet in Bioconductor 3.6.  ...
written 6 weeks ago by markus.riester20
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Comment: C: errors in version 1.7.53
... I hope this fixed now. The Mutect2 detection should be more robust and is not attempted at all if you provide the Mutect1 stats file. Can you re-try after biocLite("lima1/PureCN")? ...
written 6 weeks ago by markus.riester20
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Comment: C: errors in version 1.7.53
... Okay, never seen this before, but yes, looks like a bug. I'll try to reproduce. If you can share an example VCF (even if it only contains a single variant) that would be helpful. Thanks for the report. ...
written 6 weeks ago by markus.riester20
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Answer: A: errors in version 1.7.53
... If your VCF is generated by Mutect2, then this might be related to a bug in filterVcfMuTect2 that I just fixed yesterday in GitHub. This function is new and is supposed to filter variants by various Mutect2 flags, but wrongly removed all variants when unfiltered VCF was provided. Please note that on ...
written 6 weeks ago by markus.riester20
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Answer: A: errors in Purecn callLOH
... I fixed this bug last week in the developer version (https://github.com/lima1/PureCN/issues/10). I recommend updating to that version (requires rebuilding the normal database though). It's fairly well tested and will become new stable in 4 weeks. As workaround, you can provide the centromere positi ...
written 7 weeks ago by markus.riester20
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Comment: C: wrong output of DNAcopy::segment() for chr. with empty copy number data
... I stand corrected. I'm sure though there are other corner cases where it doesn't work with NAs, since I've stumbled across this "negative segment sizes with NAs" a few times before. But you are probably right that this is a bug worth fixing.   ...
written 12 weeks ago by markus.riester20
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Answer: A: wrong output of DNAcopy::segment() for chr. with empty copy number data
... I think you answered your question, segment() doesn't like NAs anywhere.  ...
written 3 months ago by markus.riester20
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Comment: C: Analysing TCGA Level 3 Copy Number Data Location of markers in the genome
... The level 3 TCGA data you downloaded does not provide this information. See https://cancergenome.nih.gov/abouttcga/aboutdata/datalevelstypes#11. The level 3 data is essentially the output what you would get by applying DNAcopy to level 2 data.  ...
written 4 months ago by markus.riester20
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Answer: A: Analysing TCGA Level 3 Copy Number Data Location of markers in the genome
... A segmentation algorithm like CBS in DNAcopy takes normalized copy number data along the genome and identifies breakpoints where the copy number changes. So, if I understood correctly, the TCGA data you downloaded is already segmented and there is no need for DNAcopy. If you want to generate a matri ...
written 4 months ago by markus.riester20

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