User: Eric T.

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Eric T.1.9k
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Bioinformatics at UCSF's Clinical Cancer Genomics Lab.

Posts by Eric T.

<prev • 187 results • page 1 of 19 • next >
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Answer: A: cnvkit segmetrics on multiple files
... It's not currently part of `batch`, so I'd recommend running it in a loop in Bash or a Makefile. No variation, or no reads? The latter would be an issue with mapping, the former maybe not. Which chromosomes or regions are causing trouble? I'd expect that regions close to centromeres and telomeres, ...
written 13 days ago by Eric T.1.9k
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Answer: A: Is cnvkit coverage output split into non-overlapping segments?
... Yes, the outputs should be non-overlapping if you follow the standard pipeline (e.g. "quick start" guide in the docs). Any overlapping targets are normally merged and re-subdivided as necessary in the `target` command, which is also automatically run as a step within the `batch` command. The `cover ...
written 28 days ago by Eric T.1.9k
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Answer: A: Precision of loss of heterozygosity detection with Sanger sequencing vs copy num
... To assess LOH in a tumor sample I think the "gold standard" is a SNP array, but it should be possible to get the equivalent from NGS. With the data you have, I'd call SNVs from the NGS data and look at the allele frequencies in the regions of interest. If the tumor sample is bulk tissue, the allele ...
written 6 weeks ago by Eric T.1.9k
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Comment: C: CNVkit for germline samples
... Glad to see it worked for you. Yes, you're reading the plot correctly -- the orange line shows the weighted mean of the bin log2 values within a copy number segment, and the yellow span shows the coordinates of BRCA1 as the bins are labeled in the .cnr file (which is not necessarily identical to the ...
written 7 weeks ago by Eric T.1.9k
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Answer: A: CNV calling on tumor sample with no germline counterpart
... [Canvas][1] and CNVkit can do it. [1]: https://github.com/Illumina/canvas ...
written 7 weeks ago by Eric T.1.9k
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Answer: A: Best CNV caller for Illumina WGRS data, in order to compare two phenotypes
... If these sequenced samples are germline/non-lesional tissue, good-quality (fresh or frozen, not degraded), whole genomes at 30x coverage or higher, all sequenced according to the same protocol, and you're looking for relatively small-scale deletions specific to one phenotype or the other, then consi ...
written 7 weeks ago by Eric T.1.9k
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Comment: C: CNVkit for germline samples
... The `gainloss` command doesn't do special calculations, it just slices up the .cnr and .cns files so that bins are grouped by gene name -- [see here][1]. The default threshold is a permissive log2 amplitude of +/- 0.2. I suggest loading your input BAM in IGV and looking at the read pileup at this e ...
written 7 weeks ago by Eric T.1.9k
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Comment: C: CNVkit for germline samples
... It looks like your link to the BRCA1 scatter plot didn't work, could you post the link directly? In your sample .cnr file, can you post the bin corresponding to exon 23 (matching the reference.cnn bin you posted)? I notice that in the reference, the baseline log2 value is about -.23 and the spread ...
written 8 weeks ago by Eric T.1.9k
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Answer: A: I need allele copy number information for running PyClone
... TCGA also provides copy number as SEG files, which indicate log2 ratios but not absolute integer copy number or allele-specific copy number. But you can use CNVkit along with a properly formatted VCF file to get allele-specific copy number with the `import-seg` and `call` commands. Some reformatting ...
written 8 weeks ago by Eric T.1.9k
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Answer: A: cvnkit: what is the problem here?
... To install from source in-place, I recommend using `pip install -e .` instead of `python setup.py`. Generally `conda` is best, but there's a hiccup in creating the conda package for CNVkit 0.9.0 right now. To install the dependencies manually, here's the comprehensive list: 'biopython ...
written 8 weeks ago by Eric T.1.9k

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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: When Should We Develop Biopython That Support Python 3.X?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
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