User: graeme.thorn
graeme.thorn • 50
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- London, United Kingdom
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- 5 years, 4 months ago
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Posts by graeme.thorn
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... I'm running SAM from the R samr package to in multiclass mode to determine genes differentially expressed in one or more classes, and I'm struggling to interpret the output.
I'm running it on a 5000 row by 47 sample expression matrix (either RNA-seq count or batch-corrected log-transformed express ...
written 4 days ago by
graeme.thorn • 50
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... This is likely to have been answered elsewhere, but is there a quick way to get the MSigDB gene matrix transpose (.gmt) files as Ensembl IDs rather than Entrez or HUGO symbols? ...
written 12 weeks ago by
graeme.thorn • 50
• updated
9 weeks ago by
Biostar ♦♦ 20
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... I was looking for a method sensitive enough for a single read that covers the variant ...
written 3 months ago by
graeme.thorn • 50
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... I have a list of variants that I would like to check exist in some cell-free DNA extracted from plasma. These variants arise from DNA extracted from clinical tissue, and tumour-derived variants may appear at very low levels in the cell-free DNA extracted from the same patients. The sequencing is suc ...
written 3 months ago by
graeme.thorn • 50
• updated
3 months ago by
WouterDeCoster ♦ 45k
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... I have 67 clinical tissue samples which were sequenced for RNA expression. They are in five main groups, with three of the groups linked by being triple samples from the same people taken from different locations, and the other two being taken from two groups of individuals with slightly different ...
written 4 months ago by
graeme.thorn • 50
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166
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... I have split a multi-sample vcf into each sample, and I was wondering if there was a simple method for fixing the genotype for variants to 0/1 for each single-sample vcf, and changing the alternate allele to match the new genotype. For instance, if the vcf contains a read like
`
chr1 945122 . ...
written 8 months ago by
graeme.thorn • 50
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433
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... Thanks! A quick test has shown that variations of this (see the answer) are what I required. The GATK help pages don't seem that helpful. ...
written 8 months ago by
graeme.thorn • 50
0
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433
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... As per @Pierre Lindenbaum's comment above, the correct filter for the genotype is
````vc.getGenotype("SAMPLEn").isHomRef()```` to select the "0/0" genotype and
````!vc.getGenotype("SAMPLEn").isHet() && !vc.getGenotype("SAMPLEn").isHomVar()```` to select the "0/0" or "./." genotypes.
This c ...
written 8 months ago by
graeme.thorn • 50
0
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1
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433
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1
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... I have a multisample VCF and I want to filter it based on:
1. The sequencing depth from the first sample (which is a germline sample)
and
2. The genotype of the first (and/or the third) samples (which are both germline samples)
I've been investigating ````gatk VariantFiltration```` for doing thi ...
written 8 months ago by
graeme.thorn • 50
1
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1
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229
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1
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... Are there any resources with summarised variant data from covid-19 patients who have had their genomes sequenced? The underlying sequencing data is not required, just the called variants. There are plenty of resources with viral genomes but nothing from the patients suffering from covid-19. ...
written 9 months ago by
graeme.thorn • 50
• updated
26 days ago by
Emily_Ensembl ♦ 21k
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