User: Dave Carlson

gravatar for Dave Carlson
Dave Carlson320
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320
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Location:
Stony Brook University, NY
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3 days, 11 hours ago
Joined:
4 years, 5 months ago
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d*******************@gmail.com

Posts by Dave Carlson

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Answer: A: prokka for several files at once
... I'm assuming that you want to annotate each fasta file separately. If that's correct, then you should be able to do this relatively easily with gnu parallel. According to the [github page][1], the simplest prokka usage is just: prokka Therefore, if you want to run prokka on several input f ...
written 3 months ago by Dave Carlson320
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Answer: A: repeatmasker plain text into gtf
... Note that RepeatMasker comes with a utility script to convert their default *.out file format to GFF3. You can find it at: /path/to/RepeatMasker/util/rmOutToGFF3.pl If you specifically need GTF format, you can convert using awk as Pierre suggested or using an existing tool (e.g., see [here][1 ...
written 3 months ago by Dave Carlson320
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Comment: C: Assembling haplotypes of a highly heterozygous gene cluster with canu
... I don't have any good suggestions for additional Canu parameters to tweak, but have you tried the latest version of the Platanus assembler? It's designed for heterozgous genome assembly, and uses both long and short-read data. See more here: https://www.nature.com/articles/s41467-019-09575-2 ...
written 7 months ago by Dave Carlson320
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Comment: C: Salmon RNA-seq quantification for repeated genome
... Nothing obvious to me. It might be worth running salmonTE and salmon on the same dataset (using a set of retrotransposons as the reference) and see if the results differ substantively. ...
written 7 months ago by Dave Carlson320
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Comment: C: Salmon RNA-seq quantification for repeated genome
... If you have a database of repeats for your organism, you might want consider using either [SalmonTE][1] or [TETranscripts][2] [1]: https://github.com/LiuzLab/SalmonTE [2]: https://github.com/mhammell-laboratory/TEtranscripts ...
written 7 months ago by Dave Carlson320
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Comment: C: How should I use skewer to trim paired end reads?
... I'll second this suggestion and throw in an additional plug for [fastp][1], which is also multi-threaded. [1]: https://github.com/OpenGene/fastp ...
written 7 months ago by Dave Carlson320
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Answer: A: GATK multiple samples
... You need to run HaplotypeCaller individually for each of your bam files using the "-ERC GVCF" flag. This will produce once gvcf file for each of your bam files. Then you would combine each of the GVCF files produced by HaplotypeCaller (e.g., with gatk's CombineGVCFs tool) into a single GVCF file. ...
written 8 months ago by Dave Carlson320
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Comment: C: How to make a phylogenetic tree set in ASTRAL?
... I think you will need to be more specific about your data and your goals. ASTRAL takes gene trees as input and uses these to estimate a species tree under the multi-species coalescent model (or at least a heuristic approximation). Therefore, to run ASTRAL, you would need to first infer phylogenies ...
written 8 months ago by Dave Carlson320
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Comment: C: Why wont my newick file from MEGA open in FigTree?
... You can try pasting the text of your tree file into an online viewer (e.g., [ETE Toolkit][1]), but as https://www.biostars.org/u/20598/ said, there is probably an issue with the format of the file, you should view it in a text editor. [1]: http://etetoolkit.org/treeview/ ...
written 8 months ago by Dave Carlson320
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Answer: A: Removing the last part of fasta header in many alignmnet files
... Your loop doesn't supply sed with a file to modify. This should work: for filename in *.FNA; do sed '/>/ s/\(.*\)-.*$/\1/g' $filename; done ...
written 8 months ago by Dave Carlson320

Latest awards to Dave Carlson

Voter 7 months ago, voted more than 100 times.
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
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?
Scholar 9 months ago, created an answer that has been accepted. For A: Genome duplication assessment
Popular Question 14 months ago, created a question with more than 1,000 views. For codeml jobs taking much longer on a server than on an imac
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Supporter 14 months ago, voted at least 25 times.
Popular Question 23 months ago, created a question with more than 1,000 views. For RepeatModeler finishes without creating output files
Teacher 2.8 years 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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