charlesdarwin
  • Member for 4 years, 5 months
  • Last seen more than 1 year ago
1 answers
2 votes
119 views
Why can I not install snakemake on my SLURM computer even though I can find it in the bioconda channel?
2 votes

I created a file .condarc in my home directory with the following content: channels: - conda-forge - bioconda - defaults and it works now. I don't understand why this is necessary though. I ...

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1 answers
3 votes
242 views
Error in seq.default in chromPlot
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2 votes

Using this data frame: gaps Chrom Start End Name 1 I 0 15072434 contigs 2 II 0 15279421 contigs 3 III 0 13783801 contigs 4 IV 0 17493829 contigs 5 V 0 ...

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1 answers
1 votes
121 views
How to superimpose barplots in karyotype graphic using the chromPlot Bioconductor package?
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2 votes

chromPlot(gaps = cel_gap, figCols = 2, annot1 = annot1, annot2 = annot3, annot3 = annot2, chrSide=c(1, 1, -1, 1, -1, 1, -1, 1)) The chrSide argument decides on which side the histogram goes,...

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2 answers
4 votes
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GATK CombineVariants complains the contig order in the VCF files
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GATK cannot combine VCF files generated by Sniffles, the variant caller that I used to call structural variants (answer from the GATK team).

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1 answers
3 votes
678 views
Does MinKNOW work with Mac OSX high sierra 10.13.1?
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Some replies from ONT is: OS X is supported and you can view the installation instructions on our Downloads page linked below. At the moment High Sierra is not officially supported as we have ...

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2 answers
2 votes
510 views
Joining scaffolds to get full genome?
2 votes

Ragout worked well for me. It is a reference-based scaffolder. ragout.py --outdir output/ input/ragout.rcp > message.txt 2> error.txt --threads 8 --overwrite The ragout.rcp file contains a '...

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1 answers
0 votes
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UCSC packages/tools ucsc-netchainsubset and ucsc-fatotwobit not working on GNU/Linux
1 votes

Short answer: respect the case of the tool name Longer story below Thanks to terdon, I printed the PATH when the conda environment was active and listed what was in the folder where conda installed ...

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How to uninstall hmmpress from my conda environment?
1 votes

This time conda uninstall hmmer in the root environment did the job. The sequence of commands that led me there is shown below. Thanks Devon Ryan. conda list | grep hmmer hmmer 3....

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1 answers
1 votes
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Where can I find the DNA sequence of the C. elegans rRNA cluster?
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1 votes

The info is actually in the gene_biotype column of my wormGenes data frame. I could select the rRNA genes using dplyr::filter(wormGenes, gene_biotype == 'rRNA'). Unfortunately, no description is ...

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