User: Eric T.

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Eric T.2.4k
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Location:
San Francisco, CA
Website:
http://etalog.blogspot...
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etalevich
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Last seen:
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9 years, 1 month ago
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Bioinformatics at UCSF's Clinical Cancer Genomics Lab.

Posts by Eric T.

<prev • 224 results • page 1 of 23 • next >
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Answer: A: Filtering number of markers after segmentation using DNAcopy
... Is this for research or for clinical diagnostics? Did the source data come from array CGH, SNP array, or NGS? - For research on a cohort, see if you can compare your DNAcopy results to another assay and determine the minimum segment size where the assays agree. Then, go ahead and remove small segme ...
written 4 weeks ago by Eric T.2.4k
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Answer: A: CNVkit: Dealing with noisy tumor samples
... Hi Fil, I think we've been in contact already. My suggestions so far are: - Use `metrics` on the control samples as well to remove any noisy or unsuitable samples from the copy number reference. - Use a more stringent segmentation p-value, e.g. `1e-6` - Use `segmetrics` and `call --filter ci` to re ...
written 4 weeks ago by Eric T.2.4k
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Answer: A: CNVkit Heatmap samples clustering
... CNVkit plots the samples in the order that you list the .cns files on the command. It doesn't do hierarchical clustering on its own, but if you use R or another program to e.g. hierarchically cluster the log2 values in the .cnr files, then you can observe the sample ordering there and reuse that ord ...
written 4 weeks ago by Eric T.2.4k
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Answer: A: Error in CNV Calling with Annotation
... Thanks for reporting, I've filed this issue in the project's GitHub repo: https://github.com/etal/cnvkit/issues/421 It looks like the `autobin` step here ran into a NaN when doing some basic arithmetic with bin depths to estimate a reasonable average bin size. It's surprising that `--annotate` is r ...
written 4 weeks ago by Eric T.2.4k
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Answer: A: Bootstrap function biopython
... Yes, try `Bio.Phylo.Consensus.bootstrap_trees` and `.bootstrap_consensus` to get bootstrapped tree replicates and the consensus tree, respectively. ...
written 10 weeks ago by Eric T.2.4k
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Answer: A: CNV calling from exome sequencing data with a low number of samples
... If you're looking for de novo CNVs in the proband, you can use CNVkit to build a reference from the two parent samples. The results will still be noisy, so see the "[calling][1]" and "[germline][2]" pages in the documentation for suggestions to clean up the results. [1]: https://cnvkit.readthedoc ...
written 5 months ago by Eric T.2.4k
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Comment: C: CNVkit for germline samples
... Thanks for catching this, I've updated the link above. It's now: https://github.com/etal/cnvkit/blob/master/scripts/cnv_ztest.py ...
written 5 months ago by Eric T.2.4k
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Answer: A: Running cnvkit batch with -y parameter
... If you use `-y` anywhere, you have to use it everywhere. Did the `diagram` plot come from the same `batch` run where `-y` was used? If not, you can just run `diagram` again and add `-y`. Full details here: https://cnvkit.readthedocs.io/en/stable/sex.html ...
written 6 months ago by Eric T.2.4k
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Answer: A: Best variant caller for CNVkit
... For SNVs, any variant caller that will do joint genotyping of the tumor and normal samples without dropping germline variants is fine. VarDict is good, and FreeBayes is fine too. Mutect2 unfortunately drops the germline variants, which CNVkit needs for LOH detection. See here: https://cnvkit.readthe ...
written 7 months ago by Eric T.2.4k
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Comment: C: CNVkit: gene results not in output
... OK, so far I see no reason for it to disappear. Can you track down the step in the pipeline where the gene disappears? - Are those bins actually labeled as "CCNE2" in your reference.cnn file? - After `fix`, is the CCNE2 in the output .cnr file? Are those bins (same coordinates as in the .cnn) pres ...
written 8 months ago by Eric T.2.4k

Latest awards to Eric T.

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Help with understanding CNVkit output
Popular Question 5 months ago, created a question with more than 1,000 views. For CNVkit, robust genome-wide copy number detection from DNA sequencing
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 9 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 12 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Appreciated 12 months ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?
Scholar 13 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Good Answer 17 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 17 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
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: ABSOLUTE to estimate tumour purity from WES data
Scholar 19 months ago, created an answer that has been accepted. For A: Local alignment in biopython
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 19 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 23 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Scholar 2.0 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Regarding Pseudokinases
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Regarding Pseudokinases
Scholar 2.1 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data

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