User: Eric T.

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Eric T.2.6k
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http://etalog.blogspot...
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Bioinformatics at UCSF's Clinical Cancer Genomics Lab.

Posts by Eric T.

<prev • 249 results • page 1 of 25 • next >
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Answer: A: CNVkit bwa-mem parameters
... Referring to the BWA MEM docs for posterity: http://bio-bwa.sourceforge.net/bwa.shtml Yes, secondary alignments created with -a and marked as such with -M will be handled appropriately by CNVkit, i.e. excluded from the read depth count. CNVkit calculates depth using pysam, which uses htslib interna ...
written 17 days ago by Eric T.2.6k
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Answer: A: CNVKit noisy scatter plot
... 1. Are you processing your tumor samples individually, with a pooled reference, or with matched normal samples? If this is an individual tumor samples with a flat reference, it's expected that WES will be noisy, and genemetrics for individual genes of interest based on the processed .cnr file may be ...
written 8 months ago by Eric T.2.6k
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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 17 months ago by Eric T.2.6k
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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 17 months ago by Eric T.2.6k
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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 17 months ago by Eric T.2.6k
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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 17 months ago by Eric T.2.6k
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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 17 months ago by Eric T.2.6k
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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 17 months ago by Eric T.2.6k
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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 17 months ago by Eric T.2.6k
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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 17 months ago by Eric T.2.6k

Latest awards to Eric T.

Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Tumor clonality algorithms
Teacher 17 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: Biopython PAML CodeML Error [Errno 2]
Scholar 17 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Scholar 17 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Good Answer 20 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 21 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: Local alignment in biopython
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Help with understanding CNVkit output
Popular Question 2.3 years ago, created a question with more than 1,000 views. For CNVkit, robust genome-wide copy number detection from DNA sequencing
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 2.5 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: Local alignment in biopython
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?
Scholar 2.9 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Scholar 3.0 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Good Answer 3.2 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 3.3 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 3.4 years ago, created an answer that has been accepted. For A: Local alignment in biopython
Scholar 3.4 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data

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