User: nr23

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nr2380
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Posts by nr23

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Normalise read counts between two bam files
... I just updated my question. I know that deep tools handles this, my question is, in the hypothetical example I give above, what is the appropriate way to calculate this by hand ...
written 2.9 years ago by nr2380
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Normalise read counts between two bam files
... I'm trying to calculate the read depth ratio between two bam files in a specific genomic region. One of these samples was sequenced deeper than the other - **what's the recommend way to normalise read counts between the two?** [Deeptools][1] seems like a great standalone option for normalising b ...
genome next-gen sequencing written 2.9 years ago by nr2380
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CNV-Seq read count normalisation
... I've been using [CNV-Seq][1] to detect CNV in a tumour normal pair. CNV-Seq produces 2 different files: A `.count` file, e.g.: chromosome start end test ref X 1 1000000 46775 114751 X 500001 1500000 51545 130859 X 100000 ...
genome next-gen written 2.9 years ago by nr2380
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Calculate allele frequency for structural variant breakpoints
... I have a list of high quality structural variant breakpoints that are the product of multiple different SV callers. While some of the approaches I use estimate the allele frequency for called breakpoints, others do not, so in some cases I have high quality variants that lack allele frequency estimat ...
genome next-gen written 3.0 years ago by nr2380
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Answer: A: Future direction of Gene Set Enrichment Analysis
... A good place to start: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1571-6 ...
written 3.4 years ago by nr2380
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Comment: C: How to compare a tumour sample to multiple normal samples in Freebayes
... I appreciate the comment, but this has got nothing to do with the question - of how to include a PON in Freebayes ...
written 3.4 years ago by nr2380
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Tools to filter Mutect2 output
... I've followed the GATK best practices for tumour normal somatic mutation calling with Mutect2: 1. Run Mutect2 using `--artifact_detection_mode` on each normal sample from the same sequencing run. 2. Combine all calls made in the above step into a panel of normals (PON) using `CombineVariants` ...
genome snp written 3.5 years ago by nr2380
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Comment: C: Calculate the fraction of genome that is feature X
... Thanks for taking the time to spell this out! ...
written 3.5 years ago by nr2380
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Comment: C: Calculate the fraction of genome that is feature X
... This looks like it will work for exons but not other features (5'UTR, start codon, intron) etc. Is this the case? ...
written 3.5 years ago by nr2380
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Calculate the fraction of genome that is feature X
... I am trying to calculate enrichment of Structural variant breakpoints and SNV locations in genomic features (exon, intron, 5'UTR...) in a non-human genome. To know whether a feature is over/underrepresented in a SV/SNV dataset, I first need to know the fraction of the genome that is feature X. For e ...
genome R written 3.5 years ago by nr2380

Latest awards to nr23

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Calculate allele frequency for structural variant breakpoints
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Tools to filter Mutect2 output
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Calculate the fraction of genome that is feature X
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Go In Non-Model Organisms
Supporter 2.9 years ago, voted at least 25 times.
Popular Question 6.8 years ago, created a question with more than 1,000 views. For Go In Non-Model Organisms

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