User: Peter vH

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Peter vH130
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7 years, 7 months ago
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Posts by Peter vH

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Which tools do you miss?
... This is [exonerate](https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate) but there are plenty of alternatives, e.g. [GeneWise](https://www.ebi.ac.uk/Tools/psa/genewise/), [spaln](https://github.com/ogotoh/spaln) - (manual [here](https://github.com/ogotoh/spaln)), [splign](https://www. ...
written 3 months ago by Peter vH130
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Comment: C: secondaryFiles where nameroot differs
... Thanks for the clarification about the use of expressions in contrast to bare strings with `seoncaryFiles`. I ended up with: inputs: database: type: - Directory - File label: "Kraken 2 DB" doc: "(either a File refer to the hash.k2d file in the ...
written 14 months ago by Peter vH130
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secondaryFiles where nameroot differs
... I am trying to write a wrapper for `kraken2` and struggling to express the database as a `File` with `secondaryFiles`. The structure of the DB is a directory with 3 files: `hash.k2d`, `opts.k2d` and `taxo.k2d`. Because of this structure the typical `secondaryFiles` format that assumes at least a sha ...
cwl written 14 months ago by Peter vH130 • updated 14 months ago by Michael R. Crusoe1.8k
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Comment: C: STRAW & MP-EST tree
... You provide very little to go on. STAR (http://bioinformatics.publichealth.uga.edu/SpeciesTreeAnalysis/STAR/STAR.php) seem to require Newick format (which you say you have) and a species allele file to map leaf names (in the Newick file) to species. Please provide more info with regards to your ques ...
written 15 months ago by Peter vH130
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Answer: A: Exclusive parameters in a workflow
... I implemented a solution based on my reading of what you have done: First, the tool: cwlVersion: v1.0 class: CommandLineTool inputs: touchparam: type: - type: record name: touchcode fields: touchcode: ...
written 2.5 years ago by Peter vH130
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Comment: C: BWA MEM vs BOWTIE2 , which is best?
... If you want to compare variant calling workflows, Brad Chapman's work with bcbio and comparing options might be useful to you. See: https://github.com/bcbio/bcbio_validation_workflows In essence what he did was to use the Genome in a Bottle NA12878 sample (http://jimb.stanford.edu/giab) and compare ...
written 2.7 years ago by Peter vH130
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Comment: C: intersect VCF files
... I installed `rtg-tools` 3.8.4 using bioconda. When I run `vcfeval` the output contains 4 VCFs: fn.vcf.gz fp.vcf.gz tp.vcf.gz tp-baseline.gz Judging from the slides and the preprint, the fn (false negative) file contains calls that are in the baseline but not in the calls file, the ...
written 3.0 years ago by Peter vH130 • updated 2.2 years ago by RamRS30k
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Where to find Drosophila melanogaster de novo transcript assembly data?
... I am studying de novo (non-model) genome annotation and would like to use a well characterised organism to test some of my methods. To this end I am looking for an assembled *de novo transcriptome* dataset for *Drosophila melanogaster*, preferably assembled from short read data. Does anyone know whe ...
drosophila assembly de novo transcriptome written 3.0 years ago by Peter vH130 • updated 2.4 years ago by jaudall0
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Comment: C: From multiple VCF files to multiple sequence alignment?
... So you'd do iterative vcf-consensus followed by MUSCLE? SNPhylo seems to do something like that. I'll experiment and compare it with the script I've written. ...
written 4.2 years ago by Peter vH130
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Comment: C: From multiple VCF files to multiple sequence alignment?
... I'm not quite sure how? The tools suggested in those threads, `vcf-consensus` and `FastaAlternateReferenceMaker` in the other, produce a single FASTA output from a single VCF input and don't deal with gaps created when considering the alignment between sequences having insertions and deletions. ...
written 4.2 years ago by Peter vH130

Latest awards to Peter vH

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: BWA MEM vs BOWTIE2 , which is best?
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: BWA MEM vs BOWTIE2 , which is best?
Scholar 2.5 years ago, created an answer that has been accepted. For A: Exclusive parameters in a workflow
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Using the Directory type in Common Workflow Language
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Using the Directory type in Common Workflow Language
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Example cwl workflow (for v1.0)?

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