User: Eric T.

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Eric T.2.0k
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San Francisco, CA
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http://etalog.blogspot...
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etalevich
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1 day, 15 hours ago
Joined:
8 years, 1 month ago
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Bioinformatics at UCSF's Clinical Cancer Genomics Lab.

Posts by Eric T.

<prev • 201 results • page 1 of 21 • next >
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Answer: A: Regarding Cnvkit analysis
... Off-target or "antitarget" regions are explained in the CNVkit paper here: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004873 You don't need a matched normal/control sample for the analysis, although it will usually improve your results. Some regions of the genome are no ...
written 16 days ago by Eric T.2.0k
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Comment: C: CNVkit - how many normal samples do I need for the pooled normal reference?
... Yes, that's all true, but 10-20 samples is still usually good enough to capture most of the consistent characteristics and biases of your lab process, and it lets you quickly "peek" at the results with the `batch` command without wasting much computation. For a clinical pipeline, I would recommend y ...
written 18 days ago by Eric T.2.0k
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Comment: C: tumor/normal WGS with CNVkit has many small segments with small copy number chan
... Have you used `normal.sorted_RG_noDup.bam` as a reference elsewhere? If there is something odd about the coverage in that normal sample in particular, that could shift the normalized log2 ratios for `tumor.sorted_RG_noDup.bam` -- so contamination with an enriched exome in either sample would yield s ...
written 18 days ago by Eric T.2.0k
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Answer: A: CNVkit - how many normal samples do I need for the pooled normal reference?
... You can use any number of normal samples with the [reference][1] command. You don't need access to all 110 normal samples at the same time; you can first run the [coverage][2] command twice on each BAM (once each for targets and antitargets), then collect the 'coverage' output .cnn files to use as i ...
written 21 days ago by Eric T.2.0k
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Answer: A: CNVKit - Gene labels in 'diagram'
... I've documented some suggestions for dealing with this problem here: http://cnvkit.readthedocs.io/en/latest/plots.html#reducing-cluttered-gene-labels ...
written 23 days ago by Eric T.2.0k
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Answer: A: visualize CNV data based on WGS
... You can generate a multi-page PDF of scatter plots focused on individual genomic regions (genes, chromosomes, etc.) with `cnvkit.py scatter --range-list`. At UCSF you might be able to get access to the group license for Biodiscovery Nexus Copy Number, which is commonly used by pathologists for revi ...
written 27 days ago by Eric T.2.0k
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Answer: A: tumor/normal WGS with CNVkit has many small segments with small copy number chan
... How did you run CNVkit? It looks as if it was run with two separate coverage profiles (genic and intergenic?) that were not normalized to each other when combining, so half the bins have log2 values shifted downward by 0.5. This could have happened if you ran `batch` with WGS data but did not use `- ...
written 27 days ago by Eric T.2.0k
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Answer: A: CNVKIT import errors
... This is fixed now. Sorry for the trouble, I forgot to check in a new file while refactoring. ...
written 27 days ago by Eric T.2.0k
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Answer: A: Any techniques faster than Breakdancer?
... Yes: try [LUMPY][1] or [Manta][2]. [1]: https://github.com/arq5x/lumpy-sv [2]: https://github.com/Illumina/manta ...
written 9 weeks ago by Eric T.2.0k
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Comment: C: Publicly Available Tumor/Normal Illumina Data For Evaluation Of Somatic Variant
... The sequencing data for benign, primary tumor and metastatic samples from 103 mice from [McCreery et al. 2015][1] is available through ENA: https://www.ebi.ac.uk/ena/data/view/PRJEB4767 [1]: https://www.nature.com/articles/nm.3979 ...
written 10 weeks ago by Eric T.2.0k

Latest awards to Eric T.

Scholar 27 days ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: When Should We Develop Biopython That Support Python 3.X?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 4 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 6 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Scholar 6 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Scholar 6 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 10 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Scholar 11 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Regarding Pseudokinases
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Regarding Pseudokinases
Scholar 11 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Popular Question 14 months ago, created a question with more than 1,000 views. For CNVkit, robust genome-wide copy number detection from DNA sequencing
Appreciated 14 months ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Regarding Pseudokinases
Scholar 16 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
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Scholar 19 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Scholar 19 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Regarding Pseudokinases
Scholar 20 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Voter 21 months ago, voted more than 100 times.

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