User: Brice Sarver
Brice Sarver • 3.6k
- Reputation:
- 3,570
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- United States
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- Google Scholar Page
- Last seen:
- 8 months, 1 week ago
- Joined:
- 6 years, 4 months ago
- Email:
- b***********@gmail.com
I'm a computational geneticist and bioinformatician working in industry. My background is in genomics, bioinformatics, and phylogenetics. Regularly use AWS, R, Python, bash, relational databases, and Linux HPC environments.
Posts by Brice Sarver
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4
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... Check out vcf2bed in [BEDOPS][1]. You can also try searching this site for more advice.
[1]: https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/vcf2bed.html ...
written 8 months ago by
Brice Sarver • 3.6k
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... 1. Use an assembler suitable for your data. Saying that it is paired-end isn't enough to evaluate how the libraries were prepared or what to expect. You mentioned SOAPdenovo2, so you've presumably started to explore this.
2. You can get a sense of the number of chromosomes by looking at related sp ...
written 10 months ago by
Brice Sarver • 3.6k
1
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... [AddOrReplaceReadGroups in the Picard manual][1] should tell you everything that you need to know. There's also a link to the GATK's definition list for more detailed explanations. You should also consider searching on Biostars - this has come up many times before.
[1]: http://broadinstitute.gith ...
written 10 months ago by
Brice Sarver • 3.6k
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... What you tend to see if something is out of frame is an overrepresentation of stop codons in the downstream sequences - not always, but it acts as a good flag (especially if you're only expecting one and it's at the end of the string). You can explore this by looking at the first, second, and third ...
written 11 months ago by
Brice Sarver • 3.6k
2
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378
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... What you're looking for is generally called a translation alignment. You'll start with a set of nucleotide sequences. These are converted to amino acids based on a translation table, aligned, and back-translated to their original nucleotides. This will make sure that the protein-coding genes are kep ...
written 11 months ago by
Brice Sarver • 3.6k
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... What quality metrics to look for, besides general run-specific metrics from the reads (e.g., the distribution of base qualities), will depend strongly on what's actually in the BAMs - WGS, WES, capture, amplicons, etc. For example, a high duplication rate may suggest libraries were overamplified for ...
written 11 months ago by
Brice Sarver • 3.6k
0
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1
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352
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1
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Answer:
A: Bioinformatics Server on AWS
... I'm not a web app developer, but I'll list a few things off the top of my head re: compute and storage.
You'll also need to set up a Virtual Private Cloud (VPC) and harden it using standard networking approaches. Instances are spawned into the default VPC unless another one is specified. Users and ...
written 11 months ago by
Brice Sarver • 3.6k
0
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1
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358
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... I'm not aware of an application that directly modifies the positions of the variants (alignment of indels excluded), but I'd be interested in hearing if anyone else has.
If it were me, I'd simply process the VCFs as text (it's delimited after the header), looking for a chromosome/pos/ref/alt combin ...
written 11 months ago by
Brice Sarver • 3.6k
0
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1
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481
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... Ah, misread what you had. Thanks for clarifying! ...
written 11 months ago by
Brice Sarver • 3.6k
0
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1
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481
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1
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... Check out the approach implemented in [ARC: Assembly by Reduced Complexity][1].
[1]: http://ibest.github.io/ARC/ ...
written 11 months ago by
Brice Sarver • 3.6k
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9 months ago,
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For A: 50% credibility Bayesian tree
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11 months ago,
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For A: 50% credibility Bayesian tree
Appreciated
11 months ago,
created a post with more than 5 votes.
For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
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11 months ago,
created an answer that was upvoted at least 5 times.
For A: trimming fastq files with Trimmomatic
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11 months ago,
created an answer with at least 3 up-votes.
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For A: 50% credibility Bayesian tree
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15 months ago,
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15 months ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
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For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
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15 months ago,
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16 months ago,
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16 months ago,
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For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
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17 months ago,
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17 months ago,
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17 months ago,
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For A: 50% credibility Bayesian tree
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