User: bruce.moran

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bruce.moran600
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Posts by bruce.moran

<prev • 110 results • page 1 of 11 • next >
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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 6 days ago by bruce.moran600
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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 28 days ago by bruce.moran600
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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 28 days ago by bruce.moran600
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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 4 weeks ago by bruce.moran600
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Answer: A: Microsatellite Instability, Whole exome sequencing
... There was a [good editorial][1] on MSI in JCO PO a few years ago, alongside [this paper][2] which references the set of 2,359 microsatellites in or near the exome. So reason is that not all are in non-coding regions. [1]: https://ascopubs.org/doi/full/10.1200/PO.17.00189 [2]: https://ascopubs.o ...
written 4 weeks ago by bruce.moran600
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Comment: C: low unique mapping ratio of RNA-seq data
... The `samtools view -F 256` command should output primary alignments. The [HiSat2 manual][1] states: > Each reported read or pair alignment beyond the first has the SAM > 'secondary' bit (which equals 256) set in its FLAGS field. You have paired data so it is 81,968,964/2 = 40,984,482 'primar ...
written 6 weeks ago by bruce.moran600
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Comment: C: low unique mapping ratio of RNA-seq data
... OK, can you provide the references to these papers? Would be interested to read them. Did you try the other samtools filter? Again would be interested to see how many reads are primary alignments vs. the q > 20 'unique' reads. ...
written 6 weeks ago by bruce.moran600
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Answer: A: low unique mapping ratio of RNA-seq data
... > and then use command `samtools view -q 20` to filter the unique mapped > reads From [samtools manual][1] > -q INT Skip alignments with MAPQ smaller than INT [0]. So your table shows reads with q > 20. 'Uniquely mapping' is not that helpful a term. Some reads align to more than on ...
written 6 weeks ago by bruce.moran600
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Comment: C: low unique mapping ratio of RNA-seq data
... Do you only have 4 samples? Can you post HiSat2 parameters? ...
written 6 weeks ago by bruce.moran600
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Comment: C: Unequally pooling libraries for RNAseq?
... Can use `bbsplit` from [BBmap toolset][1] to align to two genomes, common technique for example in patient-derived xenograft (PDX) where human tumour is grown in a mouse. Works well for that application in my experience. [1]: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-g ...
written 10 weeks ago by bruce.moran600

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