User: sviatoslav.kendall

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Posts by sviatoslav.kendall

<prev • 47 results • page 1 of 5 • next >
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Comment: C: Strelka2 and single tumour sample
... I think you could probably run Strelka2's germline workflow to at least find variants that differ from your reference genome. https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#germline ...
written 6 weeks ago by sviatoslav.kendall510
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Comment: C: Which Driver-Gene Detecting Software Supports hg38?
... I'm going to be looking at cancers that haven't been studied so thoroughly. I've already reached out to either the authors or people involved with maintaining the software I mentioned to ask about work-arounds and planned upgrades - haven't heard back from anyone yet. I thought this issue might ha ...
written 5 months ago by sviatoslav.kendall510
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Which Driver-Gene Detecting Software Supports hg38?
... I'm interested in detecting driver genes in some cancer biopsies that have been sequenced using hg38 as the reference. I've looked at three programs so far ([MutSig2CV][1], [MuSiC][2] and [2020+][3]) and found clear indications that two of these only support hg19 and I have not found an answer in th ...
mutsig2cv 2020+ music written 5 months ago by sviatoslav.kendall510 • updated 4 months ago by arvind.shankar30
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Can splice-site mutations be treated as gene knock-outs?
... I'm working with some exome-sequencing data that's been run through a mutation calling pipeline. My goal is determine which samples have deactivating mutations within a subset of genes. Using the [MAF][1] column "Variant_Classification", I've already decided to mutations with values like "stop_gaine ...
snp sequencing written 20 months ago by sviatoslav.kendall510 • updated 20 months ago by WouterDeCoster42k
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Filter out Non-Diploid segments in FACETS data
... I've got some sequencing data (tumor/normal pairs) that has had mutations called and also been subjected to copy number analysis using [FACETS][1]; these two analyses have been merged such that each mutation has been mapped to a FACETS segment and the associated values. I want to run an analysis t ...
R facets cnv sequencing written 2.6 years ago by sviatoslav.kendall510
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Question about Copy-Number Data produced using Sequenza
... I have a list of mutations and want to filter out mutations that are non-diploid or have been amplified or deleted. The data I'm working with had mutations called using [MuTect][1] and copy-number data produced using [Sequenza][2]. I do not have access to the raw sequencing data so I can't re-ru ...
R sequenza copy-number written 2.6 years ago by sviatoslav.kendall510 • updated 2.5 years ago by Biostar ♦♦ 20
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Answer: A: DNA differential methylation analysis for Illumina Human Methylation 450k and 27
... I think you should be OK doing that but pay attention to which reference genome you're using. I think the 27K probes might be based on an older build than the 450K. ...
written 2.7 years ago by sviatoslav.kendall510
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Answer: A: survival analysis with a continuos variable
... When I do survival analysis with a continuous variable as the predictor, I use the coxph() function something like this: coxph_obj = coxph(Surv(my_Data$Survival_Time, my_Data$Survival_Event) ~ my_Data$Continous_Variable) But here's an older post that you might find helpful: https://www.biostar ...
written 2.8 years ago by sviatoslav.kendall510
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Comment: C: Colors in IGV
... The link to IGVs default-color documentation did not work for me but it looks like it was point to [this page][1] [1]: http://software.broadinstitute.org/software/igv/AlignmentData ...
written 3.0 years ago by sviatoslav.kendall510
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SNPEFF Sequence Ontology Terms that are equivalent to a Loss of Function
... I'm writing a script that will identify loss of function mutations in a [SNPEFF][1]-annotated MAF file containing point mutations, indels or, in some cases, both. So far, I've been doing this is by typing up a list of every [Sequence Ontology][2] value that indicates a loss of function: stop_gaine ...
snp sequencing written 3.2 years ago by sviatoslav.kendall510 • updated 3.1 years ago by Biostar ♦♦ 20

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