User: Dave Carlson

gravatar for Dave Carlson
Dave Carlson390
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390
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Stony Brook University, NY
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4 years, 9 months ago
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Posts by Dave Carlson

<prev • 57 results • page 1 of 6 • next >
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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 Carlson390
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Comment: C: Gene ID's for a trinity assembled de novo transcriptome
... 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 Carlson390
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Answer: C: Gene ID's for a trinity assembled de novo transcriptome
... 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 Carlson390
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Comment: C: RNA-seq: how to handle biological replicates for differential expression analysi
... 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 Carlson390
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Compiling a list of MPI-compatible tools
... 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 ...
software mpi written 7 weeks ago by Dave Carlson390
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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 Carlson390
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Comment: C: How to remove gaps from sequence alignment?
... 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 Carlson390
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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 7 months ago by Dave Carlson390
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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 7 months ago by Dave Carlson390
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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 10 months ago by Dave Carlson390

Latest awards to Dave Carlson

Voter 11 months ago, voted more than 100 times.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Scholar 12 months ago, created an answer that has been accepted. For A: Genome duplication assessment
Popular Question 17 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 18 months ago, created an answer with at least 3 up-votes. For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Supporter 18 months ago, voted at least 25 times.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For RepeatModeler finishes without creating output files
Teacher 3.1 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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