User: Dave Carlson
Dave Carlson • 40
- Reputation:
- 40
- Status:
- New User
- Location:
- Stony Brook University, NY
- Last seen:
- 2 days, 2 hours ago
- Joined:
- 1 year, 8 months ago
- Email:
- d*******************@gmail.com
Posts by Dave Carlson
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... 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, ...
written 16 days ago by
Dave Carlson • 40
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... Good question. I'm in the same boat. What did you end up deciding to do? ...
written 8 weeks ago by
Dave Carlson • 40
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... 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 3 months ago by
Dave Carlson • 40
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... Did you ever solve this problem? I'm encountering something similar and am hoping there are answers out there. ...
written 13 months ago by
Dave Carlson • 40
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... 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 15 months ago by
Dave Carlson • 40
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... Good idea. I just ran RepeatModeler on a small subset of my data, and it worked properly, producing all the appropriate output files. ...
written 15 months ago by
Dave Carlson • 40
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... 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 ...
written 15 months ago by
Dave Carlson • 40
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... 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 20 months ago by
Dave Carlson • 40
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... 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.
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written 20 months ago by
Dave Carlson • 40
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... 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 ...
written 20 months ago by
Dave Carlson • 40
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