User: Eric T.

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

Posts by Eric T.

<prev • 248 results • page 2 of 25 • next >
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Answer: A: Weights in cnvkit cnr output
... The bin weights are correlated with the stability of the copy number signal in that bin's genomic region, as estimated from a pool of control samples (if available) and some other heuristics. In the development version of CNVkit currently on GitHub, the bin weights are more directly an estimate of ` ...
written 16 months ago by Eric T.2.6k
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Answer: A: cnvkit bgzf_read error 4 after 4 bytes
... That's odd. CNVkit reads the input BAM files with pysam, which internally uses htslib, the same as samtools. If samtools can read (e.g. index) your BAM files, then they should work fine with CNVkit. I haven't seen that error/warning myself, but if the process continues to run and the outputs from th ...
written 16 months ago by Eric T.2.6k
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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 19 months ago by Eric T.2.6k
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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 19 months ago by Eric T.2.6k
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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 19 months ago by Eric T.2.6k
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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 19 months ago by Eric T.2.6k
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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 19 months ago by Eric T.2.6k
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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 19 months ago by Eric T.2.6k
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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 19 months ago by Eric T.2.6k
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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 19 months ago by Eric T.2.6k

Latest awards to Eric T.

Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Tumor clonality algorithms
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 15 months ago, created an answer that has been accepted. For A: Biopython PAML CodeML Error [Errno 2]
Scholar 15 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Scholar 16 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Good Answer 19 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 19 months ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?
Scholar 19 months ago, created an answer that has been accepted. For A: Local alignment in biopython
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Help with understanding CNVkit output
Popular Question 2.1 years ago, created a question with more than 1,000 views. For CNVkit, robust genome-wide copy number detection from DNA sequencing
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
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
Scholar 2.5 years ago, created an answer that has been accepted. For A: Local alignment in biopython
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Appreciated 2.7 years ago, created a post with more than 5 votes. For A: When Should We Develop Biopython That Support Python 3.X?
Scholar 2.7 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
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Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Good Answer 3.1 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 3.1 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Domain Search Using Hmmer
Scholar 3.3 years ago, created an answer that has been accepted. For A: Local alignment in biopython
Scholar 3.3 years ago, created an answer that has been accepted. For A: ABSOLUTE to estimate tumour purity from WES data

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