User: Dave Carlson

gravatar for Dave Carlson
Dave Carlson40
Reputation:
40
Status:
New User
Location:
Stony Brook University, NY
Last seen:
5 days, 14 hours ago
Joined:
2 years, 5 months ago
Email:
d*******************@gmail.com

Posts by Dave Carlson

<prev • 13 results • page 1 of 2 • next >
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Comment: C: What is the -nct alternative in GATK 4.0.0.0?
... Here is what the GATK developers [say][1] about using the HaplotypeCaller Spark implementation: > This tool DOES NOT match the output of HaplotypeCaller. * * It is > still under development and should not be used for production work. * > * For evaluation only. * * Use the non-spark Haploty ...
written 6 weeks ago by Dave Carlson40
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Comment: C: What is the -nct alternative in GATK 4.0.0.0?
... Fixed, thanks. :) ...
written 6 weeks ago by Dave Carlson40
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Answer: A: What is the -nct alternative in GATK 4.0.0.0?
... As far as I know, there is no "-nct" equivalent in GATK 4. For HaplotypeCaller, even the Spark implementation is not yet recommended for use. ...
written 6 weeks ago by Dave Carlson40
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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 9 months 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 10 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 12 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 22 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 24 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 24 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 24 months ago by Dave Carlson40

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Teacher 9 months 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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