User: Brice Sarver

gravatar for Brice Sarver
Brice Sarver3.2k
Reputation:
3,230
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United States
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Last seen:
15 hours ago
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

<prev • 357 results • page 1 of 36 • next >
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Comment: C: calculating confidence intervals of boostrapped trees
... 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 Sarver3.2k
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Answer: A: .gstmp extension on .bam files downloaded from google bucket; and EOF marker is
... 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 Sarver3.2k
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Comment: C: What might be the cause of database inconsistency
... 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 Sarver3.2k
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Answer: A: New Column based on another data frame
... 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 Sarver3.2k
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Comment: C: What tool displays DNA to protein translation alignments in a text-style visuali
... Thanks - clarified above. ...
written 25 days ago by Brice Sarver3.2k
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Answer: A: What tool displays DNA to protein translation alignments in a text-style visuali
... 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 Sarver3.2k
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Comment: C: Base count NOT read count - Downsampling to specific number of bases not reads?
... 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 Sarver3.2k
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Comment: C: Base count NOT read count - Downsampling to specific number of bases not reads?
... 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 Sarver3.2k
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Comment: C: extracting info field from VCF using vcfr
... 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 Sarver3.2k
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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 Sarver3.2k

Latest awards to Brice Sarver

Scholar 13 days ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Scholar 18 days ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Scholar 22 days ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
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
Scholar 8 weeks ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Scholar 8 weeks ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
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
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

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