Samuel Lee
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Activity overview
Latest activity by Samuel Lee-
Samuel Lee commented,
Hi Garima Thakur, 1) 12 genes is a rather small panel---how many genomic bins does the panel yield? The segmentation methods in the somatic CNV pipeline are intended to be used in scenarios in whic...
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Samuel Lee commented,
Hi Indrani Datta, Unfortunately, we do not offer prebuilt PoNs, since the primary goal of building the PoN using similarly sequenced control samples is to learn patterns of sequencing bias and nois...
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Samuel Lee commented,
Hi Weichi I think that if you further crank global-psi-scale down you should start to get the desired results. For example, I set it to 1E-6 (which is probably extreme), and this yielded ploidy = 1...
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Samuel Lee commented,
Hi Weichi, Thanks for these additional questions and test results! Apologies for the delay, I took some vacation over the past few days but will return to looking at this later today. The distribut...
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Samuel Lee commented,
Thanks Weichi! And oops, one more thing—can you share your intervals file?
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Samuel Lee commented,
Thanks Weichi! That data looks pretty clean, so I think we should be able to get a good result. Perhaps some hyperparameters might need to be adjusted? Would you mind sharing that samples-by-covera...
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Samuel Lee commented,
Yes, this file must be in TSV format. I was speaking very generally about Bayesian inference https://en.wikipedia.org/wiki/Bayesian_inference. If your inferences depend very sensitively on the part...
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Samuel Lee commented,
Yes, that should be fine for an initial run. As a general principle, if your analysis is sensitive to your priors, then your data is not very informative.
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Samuel Lee commented,
Your results should hopefully not be too sensitive to the particular values used in this table—they are just priors. Typically you would not need to construct a new table for each batch unless your...
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Samuel Lee commented,
You cannot skip this step. The contig-ploidy priors table is simply a resource file that is provided to the tool. You should only need to construct this file a single time---no need to automaticall...