User: Brice Sarver

gravatar for Brice Sarver
Brice Sarver2.8k
Reputation:
2,790
Status:
Trusted
Location:
United States
Scholar ID:
Google Scholar Page
Last seen:
3 hours ago
Joined:
4 years, 11 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

<prev • 298 results • page 2 of 30 • next >
1
vote
1
answer
116
views
1
answers
Comment: C: Is it a problem that the reference genome is not at the chromosome level?
... You could also attempt to localize scaffolds to closely-related species with more sophisticated references using BLAT, if LiftOver (or CrossMap or your favorite alternative) won't work because there's no good whole-genome alignments to create a chainfile. This will work best if the scaffolds are sho ...
written 14 days ago by Brice Sarver2.8k
2
votes
1
answer
116
views
1
answers
Answer: A: Is it a problem that the reference genome is not at the chromosome level?
... All bioinformatic applications, including mapping (to a FASTA), will proceed as usual. For annotation, you'll also be fine as long as the contig/scaffold names are the same as the annotation file you're using. This isn't a major problem - the human reference, for example, has a number of unlocalized ...
written 14 days ago by Brice Sarver2.8k
1
vote
1
answer
109
views
1
answers
Answer: A: Creating consense tree using bootstrap value support not majority rule
... From discussion in the comments above: For a rapid, quartet-based approach, check out [ASTRAL][1]. For a fully Bayesian implementation, check out *BEAST or SNAPP, implemented in [BEAST2][2], depending on how your data are structured. You can also check out [BPP][3]. There are other approaches that ...
written 17 days ago by Brice Sarver2.8k
0
votes
1
answer
90
views
1
answers
Answer: A: GATK VariantFiltration NumberFormatException
... The GATK is particularly sensitive to type, and you can get weird results if you try to mix-and-match among them. Perhaps the more relevant question is why your DP fields are `''`. If you don't have a depth of at least 1, how do you have any evidence for that site to potentially harbor a variant in ...
written 18 days ago by Brice Sarver2.8k
0
votes
1
answer
109
views
1
answers
Comment: C: Creating consense tree using bootstrap value support not majority rule
... By different reference sequences, I'm assuming you mean different loci but the same individuals? This is a perfect candidate for species tree approaches, which attempt to account for discordance among loci due to a number of factors (depending on the approach) and estimates the species tree given a ...
written 18 days ago by Brice Sarver2.8k
0
votes
0
answers
81
views
0
answers
Comment: C: Hwo to do quality control steps on UKBiobank data?
... Entirely depends on the study. I would recommend thinking about what you're trying to accomplish and exploring the literature for meaningful filtering approaches depending on what you want to do. ...
written 19 days ago by Brice Sarver2.8k
1
vote
1
answer
109
views
1
answers
Comment: C: Creating consense tree using bootstrap value support not majority rule
... You need to clarify substantially and/or may be confused about what a consensus tree actually is. Are you concatenating Newick trees and treating them as bootstrap replicates, or have you actually performed bootstrap replicates? Where does this come into play? I can provide suggestions in a comment ...
written 19 days ago by Brice Sarver2.8k
0
votes
1
answer
111
views
1
answers
Comment: C: Integrating gene expression (RNA-Seq), mutations and patient survival data
... I'm assuming you've seen [this paper that just came out this week][1] (and are doing a follow-up on DNMT3A?). Have you considered exploring what they did? It's similar to what you want to do. [1]: https://www.cell.com/cell-reports/fulltext/S2211-1247(19)30885-X ...
written 20 days ago by Brice Sarver2.8k
0
votes
0
answers
8
views
0
answers
Comment: C: What is DESeq2 factor?
... Factor, as in, "What does a factor mean in the context of DESeq2 in R?" Or something else? ...
written 21 days ago by Brice Sarver2.8k
0
votes
1
answer
89
views
1
answers
Answer: A: How to find matching strings from two files, and if they match take the whole li
... A function across positions will be cleaner. Using `rbindlist()` from data.table and `lapply()`to make clean results. Several specifics will need to be changed (arguments to `read.table()` like sep, header, etc., most likely. This is one solution that doesn't explicitly use for loops (but is doing a ...
written 22 days ago by Brice Sarver2.8k

Latest awards to Brice Sarver

Scholar 5 days ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Scholar 13 days 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 5 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Teacher 9 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
Scholar 9 months ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Identifying degenerate positions in Mus
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: trimming fastq files with Trimmomatic
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Quickly subsetting VCF while being memory efficient
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: trimming fastq files with Trimmomatic
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: split supermatrix by gene
Teacher 2.5 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
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Software for evaluating multiple sequence alignments before phylogenetic analysi
Teacher 2.5 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 2.7 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
Scholar 2.8 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 2.9 years ago, created an answer with at least 3 up-votes. For A: 50% credibility Bayesian tree
Scholar 2.9 years ago, created an answer that has been accepted. For A: 50% credibility Bayesian tree

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1073 users visited in the last hour