User: Dave Carlson

gravatar for Dave Carlson
Dave Carlson40
Reputation:
40
Status:
New User
Location:
Stony Brook University, NY
Last seen:
1 day, 4 hours ago
Joined:
1 year, 10 months ago
Email:
d*******************@gmail.com

Posts by Dave Carlson

<prev • 10 results • page 1 of 1 • next >
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Strategies for calling variants in a transposon-rich genome
... Hi All, I'm trying to call variants in a set of plant genome samples using a bwa mem followed by GATK's HaplotypeCaller. However, I'm running into a potential roadblock that I'm hoping to get advice on. These genomes are rich in transposable elements, and when I visualize the alignments with IGV, ...
genome gatk snp written 10 weeks ago by Dave Carlson40
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Answer: A: When running MITE-hunter, can I split the input genome?
... Good question. I'm in the same boat. What did you end up deciding to do? ...
written 3 months ago by Dave Carlson40
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Answer: A: Positive Darwinian selection and Codon based Z test
... One way to look for positive selection between two sequences is to examine the abundance of synonymous and non-synonymous substitutions present. Under a scenario of neutral evolution (i.e., where selection on the sequence is weak or non-existent and genetic drift is likely the main evolutionary dri ...
written 5 months ago by Dave Carlson40
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Comment: C: Repeatmodeler Error (Error Index Out Of Bounds!)
... Did you ever solve this problem? I'm encountering something similar and am hoping there are answers out there. ...
written 15 months ago by Dave Carlson40
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Comment: C: RepeatModeler finishes without creating output files
... Thanks. I'm running it again, specifically writing stdout/stderr to file this time. Hopefully if things still don't work properly, I'll have more info this time. Appreciate the suggestions! ...
written 17 months ago by Dave Carlson40
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Comment: C: RepeatModeler finishes without creating output files
... Good idea. I just ran RepeatModeler on a small subset of my data, and it worked properly, producing all the appropriate output files. ...
written 17 months ago by Dave Carlson40
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RepeatModeler finishes without creating output files
... Hi All, I am running RepeatModeler on a ~300 mb plant genome assembly to annotate transposable elements. The program successfully runs without error but it doesn't produce the "consensi.fa.classified" output file, and the "consensi.fa" file is empty. I find it highly unlikely that my genome assem ...
repeatmodeler written 17 months ago by Dave Carlson40
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Answer: A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
... If you plan on using Trinity, their website has a great deal of valuable information.  I found it quite helpful in the past: https://github.com/trinityrnaseq/trinityrnaseq/wiki ...
written 22 months ago by Dave Carlson40
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Comment: C: Has anyone used BP&P (Bayesian phylogenetics and phylogeography)?
... I've used it for species delimitation analyses, although it's been a while.  It would be helpful if you could be more specific regarding what kind of advice you're looking for. ...
written 22 months ago by Dave Carlson40
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codeml jobs taking much longer on a server than on an imac
... Hi All, First time Biostar poster here with a question that is baffling me.  I'm using codeml to test for positive selection on a 6 taxa phylogeny using about 2000 alignments.  I'm running some of these analyses on a lab server and some of them on an imac (specs for both listed below), but there ar ...
latest sequence codeml written 22 months ago by Dave Carlson40

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Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?

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