User: bruce.moran

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bruce.moran650
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Posts by bruce.moran

<prev • 116 results • page 1 of 12 • next >
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Comment: C: How to download BCL files from NextSeq run?
... Old thread, but can you specify how you got to BCL through basemount? ...
written 9 weeks ago by bruce.moran650
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Answer: A: How to find those files name which contains specific symbol i.e. underscore sign
... > so now i want to extract those files names (like abc00001.keg) which don’t contains underscore sign _ in 2nd column of each files. for x in *.keg; do TEST=$(cut -f 2 $x | grep _ | head -n1) if [[ $TEST == "" ]];then echo $x; fi done ...
written 10 weeks ago by bruce.moran650
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Comment: C: Need help understanding ARACNe-AP output
... You need to find 'master regulators' using for example [viper][1] [1]: https://www.bioconductor.org/packages/release/bioc/html/viper.html ...
written 3 months ago by bruce.moran650
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Comment: C: Ploidy for variant calling in tumor pooled samples for amplicon next-generation
... For both MuTect2, HaplotypeCaller (no experience with FreeBayes) > Ploidy per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy). So DNA was pooled, libraries made and sequenced? The four tumours are all from the same individual? Is the amplicon panel only on the ...
written 5 months ago by bruce.moran650
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Comment: C: GATK4 VariantRecalibrator resource error
... Don't do much germline mutation calling, but I think ExAC might have superseded HapMap? No idea WRT `-comp`. I highly recommend [the GATK website][1], it's a bit of a mess because of versioning but the users and mods are very active, and because it's GATK your error will have occurred for others and ...
written 5 months ago by bruce.moran650
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Comment: C: GATK4 VariantRecalibrator resource error
... Have a look at [this thread][1] Basically you need a `:` between resource parameters and the resource path: --resource hapmap,VCF,known=false,training=true,truth=true,prior=15.0:/xxx/REFERENCES/hg19/hapmap_3.3.hg19.sites.reorder.vcf Although this also depends on your version of GATK... [1]: ...
written 6 months ago by bruce.moran650
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Answer: C: Post-filtering WES for mutation calling
... Most GATK tools have the [--intervals (-L) flag][1] which allows you to input a file of the regions that you are interested in, i.e. your exome. That is the stage at which I usually reduce to the region of interest. My rationale is that copy number callers can sometimes use off-target reads from e ...
written 7 months ago by bruce.moran650
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Comment: C: How to calculate Tumor Mutation Burden (TMB) for TCGA samples
... For a conservative estimate, I use non-synonymous mutations, but [the recent MSK-IMPACT paper][1] used all somatic muatations: > Mutational-load assessment and statistical analysis. The total number > of somatic mutations identified was normalized to the exonic coverage > of the respective ...
written 7 months ago by bruce.moran650
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Answer: C: How to calculate Tumor Mutation Burden (TMB) for TCGA samples
... Mutational load is more a population genetics term IIRC, whereas TMB is specific to somatic variants. To calculate TMB, you need to know the total size of the region sequenced. If data is from exome sequencing, you would find the size of the exome capture, and divide total mutations (or non-synony ...
written 7 months ago by bruce.moran650
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Comment: C: Microsatellite Instability, Whole exome sequencing
... Because microsatellites are so highly variable per individual, I think you will need matched normal to test MSI. Without matched normal you could investigate tumour mutational burden (TMB). ...
written 8 months ago by bruce.moran650

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