User: graeme.thorn

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graeme.thorn50
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London, United Kingdom
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Posts by graeme.thorn

<prev • 58 results • page 1 of 6 • next >
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How to interpret output of SAM/SAMseq in R (samr package)
... 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 ...
R written 4 days ago by graeme.thorn50
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MSigDB gmt files with Ensembl ID identifiers
... 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? ...
msigdb written 12 weeks ago by graeme.thorn50 • updated 9 weeks ago by Biostar ♦♦ 20
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Comment: C: Mutation calling directly from FASTQ files
... I was looking for a method sensitive enough for a single read that covers the variant ...
written 3 months ago by graeme.thorn50
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Mutation calling directly from FASTQ files
... 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 ...
variant calling dna-seq written 3 months ago by graeme.thorn50 • updated 3 months ago by WouterDeCoster45k
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PCA on exon count data
... 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 ...
R splicing rna-seq written 4 months ago by graeme.thorn50
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Fixing genotypes from split vcf
... 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 . ...
vcf written 8 months ago by graeme.thorn50
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Comment: C: GATK VariantFiltration multiple filters including genotype for multi-sample VCF
... 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.thorn50
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Answer: A: GATK VariantFiltration multiple filters including genotype for multi-sample VCF
... 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.thorn50
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GATK VariantFiltration multiple filters including genotype for multi-sample VCF
... 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 ...
vcf gatk written 8 months ago by graeme.thorn50
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Variant data from covid-19 patients
... 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. ...
vcf covid-19 written 9 months ago by graeme.thorn50 • updated 26 days ago by Emily_Ensembl21k

Latest awards to graeme.thorn

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Popular Question 9 months ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 16 months ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Popular Question 21 months ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 23 months ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 2.4 years ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: TCGA (legacy) barcodes for identifying tumour/normal samples
Scholar 2.6 years ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Error in GSNAP - unable to find genome in directory
Scholar 5.2 years ago, created an answer that has been accepted. For A: Error in GSNAP - unable to find genome in directory

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