User: Brice Sarver
Brice Sarver • 2.6k
- Reputation:
- 2,620
- Status:
- Trusted
- Location:
- United States
- Scholar ID:
- Google Scholar Page
- Last seen:
- an hour ago
- Joined:
- 4 years, 10 months ago
- Email:
- b***********@gmail.com
I'm a computational geneticist and bioinformatician working in industry. My background is in genomics, bioinformatics, and phylogenetics. AWS, R, Python, bash, relational databases, and Linux HPC environments.
Posts by Brice Sarver
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... 1) Do you have enough variability in your sequences?
2) Are you providing enough sequences at an appropriate tree height to expect to recover anything?
3) You're allowing more than one ratio among branches (model = 2) yet assuming a single rate among sites (NSsites = 0). Is this what you're trying t ...
written 4 hours ago by
Brice Sarver • 2.6k
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... Hopping in to provide support for ATpoint's comments - they're right. Map to the whole genome, then subset or restrict variant calling to regions of interest. You want your mapping qualities to reflect any uncertainty in genomic placement to produce the most accurate variant calls for your regions o ...
written 4 hours ago by
Brice Sarver • 2.6k
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... So, you have multiple sequences with different start points relative to one another? Do you need to perform a multiple sequence alignment before translation, or has this already been done? ...
written 1 day ago by
Brice Sarver • 2.6k
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... Paging [Zev.Kronenberg][1].
[1]: https://www.biostars.org/u/3153/ ...
written 5 days ago by
Brice Sarver • 2.6k
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... Have you tried defining PL in the header with your favorite plain text editor or using [bcftools reheader][1]?
[1]: http://www.htslib.org/doc/bcftools.html#reheader ...
written 29 days ago by
Brice Sarver • 2.6k
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... [bcftools view][1] will do this quickly and easily.
[1]: http://www.htslib.org/doc/bcftools.html#view ...
written 29 days ago by
Brice Sarver • 2.6k
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... Not enough information is given, but it sounds like they either want to subset or merge. Jean-Karim is right in this should likely be closed as off-topic. On the off chance that this is simply subsetting a large results file (say, ignoring headers), see below.
Using data tables below, though data f ...
written 29 days ago by
Brice Sarver • 2.6k
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... You're getting a permission denied error - have you confirmed that your ID and key have the appropriate privileges for the bucket and/or whether there are any other restrictions placed on the object?
Can you see it if you use the AWS CLI (e.g., `aws s3 ls ...`? Do you need to change the [region for ...
written 4 weeks ago by
Brice Sarver • 2.6k
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... Are you aligning alignments or constructing MSAs from batches of genes/genomes? What's your input size? ...
written 4 weeks ago by
Brice Sarver • 2.6k
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Comment:
C: paired reads have different names
... Agreed. mm, please provide the BWA call. One input FASTQ or two? ...
written 4 months ago by
Brice Sarver • 2.6k
Latest awards to Brice Sarver
Appreciated
26 days ago,
created a post with more than 5 votes.
For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
Teacher
8 weeks ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
4 months ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Scholar
8 months ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: How to construct a tree with MEGA when some of the sequences are very short
Teacher
2.4 years ago,
created an answer with at least 3 up-votes.
For A: Software for evaluating multiple sequence alignments before phylogenetic analysi
Teacher
2.4 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Teacher
2.4 years ago,
created an answer with at least 3 up-votes.
For A: How to construct a tree with MEGA when some of the sequences are very short
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Identifying degenerate positions in Mus
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Quickly subsetting VCF while being memory efficient
Appreciated
2.4 years ago,
created a post with more than 5 votes.
For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
Teacher
2.4 years ago,
created an answer with at least 3 up-votes.
For A: The nucleotides on ENST00000347310 and ENST00000425614 do not agree on the same
Good Answer
2.4 years ago,
created an answer that was upvoted at least 5 times.
For A: trimming fastq files with Trimmomatic
Appreciated
2.4 years ago,
created a post with more than 5 votes.
For A: trimming fastq files with Trimmomatic
Teacher
2.6 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Teacher
2.7 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Teacher
2.8 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Teacher
2.8 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Teacher
2.8 years ago,
created an answer with at least 3 up-votes.
For A: How to construct a tree with MEGA when some of the sequences are very short
Teacher
2.8 years ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: Is there any way to quantify differences between neighbour-joining phylogenetic
Scholar
2.8 years ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
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