User: Brice Sarver
Brice Sarver • 3.2k
- Reputation:
- 3,230
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- United States
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- Last seen:
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- Joined:
- 5 years, 2 months ago
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- 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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... Upvoting, plus some additional thoughts.
You have a tree, and you're interested in support values from a distribution of trees you've already generated (regardless of approach). You want to make a consensus tree (perhaps majority-rule to account for any uncertainty in your point estimate?), and you ...
written 12 days ago by
Brice Sarver • 3.2k
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... The temporary extension likely means something went wrong, but Samtools' `quickcheck` will tell you if the BAM is valid. From the manual:
> samtools quickcheck [options] in.sam|in.bam|in.cram [ ... ]
>
> Quickly check that input files appear to be intact. Checks that
> beginning of the ...
written 19 days ago by
Brice Sarver • 3.2k
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... Sometimes chromosome/contig/scaffold names differ among sources (e.g., 1 vs. chr1 vs. NC_000001 vs. NC_000001.11). ...
written 20 days ago by
Brice Sarver • 3.2k
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... Something like this will work. Assumes non-overlapping domains and no special R packages. Also casting to numerics to avoid any character conflicts. ranges must be global.
locate_domain <- function(position) {
for (i in 1:nrow(ranges)) {
r <- c(as.numeric(ranges[i, 1]):as.numer ...
written 21 days ago by
Brice Sarver • 3.2k
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... Thanks - clarified above. ...
written 25 days ago by
Brice Sarver • 3.2k
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... If by 'aligned to translations' you mean 'converted to translation,' you can look into [Geneious][1]. I recall it has a view below the sequence of all translation frames (e.g., 0, +1, +2). It looks like [Jalview][2] will do this, too.
Geneious Prime is currently subscription-based for academic and ...
written 25 days ago by
Brice Sarver • 3.2k
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... Thanks for clarifying. I've never seen an absolute requirement this stringent, so I was just curious as to the purpose. Genomax' solution below is a good starting place. ...
written 25 days ago by
Brice Sarver • 3.2k
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... So...your plan is to map, look at per-base coverage across a set of targets or something, then downsample the reads so you have an absolute known coverage with zero variability? I'm confused by your calculations - are you just saying that sample 1 has X reads so, given a mean length of Y bases/read, ...
written 26 days ago by
Brice Sarver • 3.2k
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... Why not write an expression to sub out the colons in the INFO field and replace with semicolons?
Edit: the justification for this suggestion, from the VCF specification -
>INFO - additional information: (String, no white-space, semi-colons, or equals-signs permitted; commas are
permitted only a ...
written 26 days ago by
Brice Sarver • 3.2k
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Comment:
C: Need help with codeml
... Those sets of nested models are looking at slightly different things. The M7 vs. M8 and M8 vs. M8a comparisons are the best for identifying signatures of positive selection, with the M8 vs. M8a comparison (a ω = 1 class in M8a) yielding fewer false positives.
Remember that you're *selecting among ...
written 26 days ago by
Brice Sarver • 3.2k
Latest awards to Brice Sarver
Teacher
28 days ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Teacher
29 days ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Appreciated
5 weeks 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
Appreciated
11 weeks ago,
created a post with more than 5 votes.
For A: Looking for a maximum parsimony tree-builder with bootstrapping that can be run
Scholar
12 weeks ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Teacher
12 weeks ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
12 weeks ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Scholar
3 months ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
3 months ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Appreciated
4 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
Teacher
5 months ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Scholar
8 months ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Scholar
12 months ago,
created an answer that has been accepted.
For A: 50% credibility Bayesian tree
Teacher
12 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
12 months ago,
created an answer with at least 3 up-votes.
For A: 50% credibility Bayesian tree
Appreciated
2.8 years ago,
created a post with more than 5 votes.
For A: trimming fastq files with Trimmomatic
Appreciated
2.8 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
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