User: Eric T.

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Eric T.2.5k
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Bioinformatics at UCSF's Clinical Cancer Genomics Lab.

Posts by Eric T.

<prev • 248 results • page 1 of 25 • next >
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Comment: C: CNVkit - diagram problem
... The decimal issue you're showing here is very strange. I'm thinking: - Why is `` 477_192314_7516-XRCC2_1`` from chr7 listed in the middle of these BRCA1 targets? The other targets here don't appear to be in genomic order, either. If the .cnn or .cnr files are scrambled, then that could lead to othe ...
written 3 months ago by Eric T.2.5k
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Answer: A: CNVKIT - unable to produce scatter and diagram pdfs
... It could be that numpy or pandas became more stringent in a recent release and so datapoints that used to pass through are now being dropped or set to NA -- just speculating. There are some changes worth considering in the development version of CNVkit, v0.9.7.dev0 or so. (The master branch on gith ...
written 3 months ago by Eric T.2.5k
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Comment: C: Noisy CNV background in old FFPE sample
... The molecules don't exactly disappear, but after shearing a larger fraction of the remaining fragments will be too small (e.g. <200bp) and will be lost during wet-lab processing and sequencing, I think. ...
written 3 months ago by Eric T.2.5k
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Answer: A: UK Biobank reference genome?
... The [exomes][1] are aligned to GRCh38 with the "chr" prefix removed from the sequence names. The older [SNP array genotypes][2], as Kevin noted, use GRCh37 as the reference. [1]: https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=170 [2]: https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=26 ...
written 3 months ago by Eric T.2.5k
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Answer: A: UK Biobank l2r data holds segment means but no segment locations?
... My understanding is that the UK Biobank `l2r` files are the copy ratio estimates at each probe in the SNP array -- they have not been segmented in the publicly available dataset, so there are no segment breakpoints. There are a couple of papers that survey CNVs; they used PennCNV on these input fil ...
written 3 months ago by Eric T.2.5k
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Answer: A: CNV analysis for tumor panel
... CNVkit tends to work well on tumor panels and is easy to use. ...
written 3 months ago by Eric T.2.5k
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Answer: A: CNVkit - diagram problem
... Are the parentheses really there in the gene name? Are there spaces, too? Maybe the formatting gets strange when it goes through PDF rendering by reportlab. Are you using the .cnr, the .cns, or both with the `diagram` command? Which version of CNVkit are you using? When pandas writes out the .cnn ...
written 3 months ago by Eric T.2.5k
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Comment: C: CNVKIT - unable to produce scatter and diagram pdfs
... If probes.bed indicates the captured regions, I'd go with that over targets.bed for CNV calling -- not all of the requested targets may have been successfully captured by the panel kit. ...
written 3 months ago by Eric T.2.5k
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Answer: A: Noisy CNV background in old FFPE sample
... The samples' DNA may have degraded to the point where you're reading relatively few unique sequence fragments in your sequencing runs of these samples, so regardless of PCR amplification, the deduplicated coverage depth of the aligned reads is lower than you need for accurate CNV estimation. Depend ...
written 3 months ago by Eric T.2.5k
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Answer: A: Weights in cnvkit cnr output
... The bin weights are correlated with the stability of the copy number signal in that bin's genomic region, as estimated from a pool of control samples (if available) and some other heuristics. In the development version of CNVkit currently on GitHub, the bin weights are more directly an estimate of ` ...
written 3 months ago by Eric T.2.5k

Latest awards to Eric T.

Scholar 3 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: When Should We Develop Biopython That Support Python 3.X?
Appreciated 7 months ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?
Scholar 7 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Help with understanding CNVkit output
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Popular Question 13 months ago, created a question with more than 1,000 views. For CNVkit, robust genome-wide copy number detection from DNA sequencing
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 17 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 20 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Appreciated 20 months ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?
Scholar 21 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: When Should We Develop Biopython That Support Python 3.X?
Scholar 2.1 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 2.3 years ago, created an answer that has been accepted. For A: Local alignment in biopython
Scholar 2.3 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Scholar 2.3 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 2.6 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data

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