User: Dave Carlson
Dave Carlson • 390
- Reputation:
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- Stony Brook University, NY
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- 1 day, 9 hours ago
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- 4 years, 9 months ago
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Posts by Dave Carlson
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Answer:
A: vcf format to Mapmaker format
... Old thread, but I've been learning OneMap recently and wanted to note that OneMap can now take a vcfR object as input. The steps to make this work would be
library(vcfR)
library(onemap)
# read in vcf file
myvcf <- read.vcfR("/path/to/myvcf")
...
written 11 days ago by
Dave Carlson • 390
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... I've used dammit before. It's very fast and easy to use. I think I like Trinotate better, though, mostly because it providers a somewhat wider set of annotation types and because of the integration with Trinity that you mentioned. ...
written 5 weeks ago by
Dave Carlson • 390
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... Note that Maker is used for gene prediction from whole genome assemblies (often using transcriptomes in the process). If all you have is the transcriptome assembly, something like Trinotate ([LINK][1]) might be a more appropriate choice.
[1]: https://github.com/Trinotate/Trinotate.github.io/wik ...
written 5 weeks ago by
Dave Carlson • 390
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... To this excellent answer I just wanted to add that DESeq2 has many useful and detailed tutorials. For example:
http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html ...
written 6 weeks ago by
Dave Carlson • 390
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... Hi All,
I do some work for my university's HPC cluster, and I was thinking it might be useful to compile a list of bioinformatics tools that are capable of parallel processing across multiple compute nodes via MPI. Historically, I think that most widely used tools have been single-node only, but th ...
written 7 weeks ago by
Dave Carlson • 390
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Answer:
A: bowtie2 maximum value of MAPQ
... As noted in both the sources that [RamRS][1] provided in his linked comment, the max MAPQ score that bowtie2 gives is 42. You should be able to demonstrate this for yourself by examining the distribution of MAPQ scores from your own data.
[1]: https://www.biostars.org/u/8494/ ...
written 9 weeks ago by
Dave Carlson • 390
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... If you literally remove all the gaps, it will no longer be an alignment. It will just be a multi-fasta file. Is that what you want? Or are you looking to remove positions/columns in the alignment file that include gaps? This would preserve the structure of alignment, at the cost of removing some ...
written 9 weeks ago by
Dave Carlson • 390
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... 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 7 months ago by
Dave Carlson • 390
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... 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 7 months ago by
Dave Carlson • 390
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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 10 months ago by
Dave Carlson • 390
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For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
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For codeml jobs taking much longer on a server than on an imac
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