User: Dave Carlson
Dave Carlson • 290
- Reputation:
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- Stony Brook University, NY
- Last seen:
- 16 hours ago
- Joined:
- 3 years, 10 months ago
- Email:
- d*******************@gmail.com
Posts by Dave Carlson
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... 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 11 days ago by
Dave Carlson • 290
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... 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 13 days ago by
Dave Carlson • 290
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... 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 14 days ago by
Dave Carlson • 290
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... 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 18 days ago by
Dave Carlson • 290
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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 5 weeks ago by
Dave Carlson • 290
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... 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 6 weeks ago by
Dave Carlson • 290
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... 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 6 weeks ago by
Dave Carlson • 290
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... 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 6 weeks ago by
Dave Carlson • 290
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Comment:
C: how to use Ka/Ks calculator
... Are you referring to the Ka/Ks calculator found here?
[https://kakscalculator.herokuapp.com/][1]
[1]: https://kakscalculator.herokuapp.com/ ...
written 7 weeks ago by
Dave Carlson • 290
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... How about:
sed 's/^>[A-Z0-9]\+.[0-9] Archilochus alexandri />BCH /' seq.fasta > new_seq.fasta
Using your examples, this will produce:
>BCH voucher B02923 cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial
GGCTGGAATAGTTGGAACCTCTCTAAGCCTACTAATCCGAGCGGAACTCGG ...
written 7 weeks ago by
Dave Carlson • 290
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For codeml jobs taking much longer on a server than on an imac
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