User: Eric T.

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Eric T.2.5k
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San Francisco, CA
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http://etalog.blogspot...
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etalevich
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Joined:
9 years, 6 months ago
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Bioinformatics at UCSF's Clinical Cancer Genomics Lab.

Posts by Eric T.

<prev • 237 results • page 1 of 24 • next >
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Answer: A: No CNV calls in CNVkit import-rna
... It looks like there was a regression and `import-rna` is currently only working for RSEM files, not the 2-column format: https://github.com/etal/cnvkit/issues/425 Working on a fix. ...
written 11 weeks ago by Eric T.2.5k
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Comment: C: I got a problem with making normal reference using cnvkit
... I suggest adding the `target` command with a bin size of 5000 after step 1, then use the resulting BED file as input to the `coverage` command. Otherwise the bins will be huge. ...
written 12 weeks ago by Eric T.2.5k
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Comment: C: CNVkit output problem: Is "log2" the same as "Seg_mean"? OR how can I get "Seg_m
... Hmm, not sure, I'll take a look to see if there's a bug in `guess_baits.py`. If you're building a pooled reference (multiple control samples), you can also just use the refflat.bed file as-is and CNVkit will drop most of the uncaptured exons automatically. ...
written 12 weeks ago by Eric T.2.5k
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Comment: C: CNVkit output problem: Is "log2" the same as "Seg_mean"? OR how can I get "Seg_m
... For exome, `-m hybrid` is better than `-m amplicon`. You can verify that there are off-target reads by loading the BAM file in a viewer like IGV. For `guess_baits.py`, try UCSC's RefSeq exons (refFlat.txt [here][1]), or another BED file of known genes from UCSC Genome Browser. Make sure the referen ...
written 3 months ago by Eric T.2.5k
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Answer: A: CNVkit output problem: Is "log2" the same as "Seg_mean"? OR how can I get "Seg_m
... xxxxxxxxxxxxxxxxxxxx ...
written 3 months ago by Eric T.2.5k
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Answer: A: CNVkit for somatic copy number detection
... For `autobin`, use normal samples. If you have at least 5 or so normal samples prepared according to the same lab process, use those as a single pooled reference for your cohort. You can probably assume that the CNV calls you get from the default pipeline are somatic. Population-level CNVs are typi ...
written 3 months ago by Eric T.2.5k
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Answer: A: I got a problem with making normal reference using cnvkit
... The `autobin` command is meant to be run just once per cohort, using a representative sample (e.g. GroupA_Normal). It looks at the on- and off-target coverage depths of that sample to choose reasonable bin sizes, and then generates corresponding bin coordinates as BED files. For processing multiple ...
written 3 months ago by Eric T.2.5k
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Comment: C: CNVkit- weird results when using the same sample as normal
... This is expected. CNVkit doesn't directly subtract the normal from the test sample; the normal sample is one of several factors that go into the final calls. ...
written 3 months ago by Eric T.2.5k
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Comment: C: scatter plots with single chromosome gives IndexError
... Thanks, I've fixed the link. I don't know if v0.9.6 has landed on bioconda yet, but 0.9.6.dev0 is the development release prior to the stable 0.9.6 release, and the latter is the one you want. You can `pip install` it directly from GitHub and it should work if you've already installed the R depende ...
written 3 months ago by Eric T.2.5k
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Answer: A: scatter plots with single chromosome gives IndexError
... This is now fixed in [CNVkit version 0.9.6][1]. [1]: https://github.com/etal/cnvkit/releases/tag/v0.9.6 ...
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
Appreciated 3 months ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Help with understanding CNVkit output
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Popular Question 9 months ago, created a question with more than 1,000 views. For CNVkit, robust genome-wide copy number detection from DNA sequencing
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 14 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Appreciated 16 months ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?
Scholar 16 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Scholar 18 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Good Answer 21 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 21 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 21 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Scholar 23 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Scholar 23 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 24 months ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 2.2 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: ABSOLUTE to estimate tumour purity from WES data
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Regarding Pseudokinases
Scholar 2.4 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data

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