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Related tickets/PRs:
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- [ ] To-do: 6/6 request that charts are used in the next tutorial revision to replace the Plotting tool. Needs training-repo ticket if confirmed a yes (some discuss…
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I'm attempting to run Atlas on a TORQUE cluster with a different data storage area than my home dir containing snakemake and conda files. Not sure if this is too similar to #95 but the snakemake rule …
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Hi,
I am running the DigitalExpression tool (v1.13) but I am encountering an issue:
```
[Wed Sep 26 18:33:04 UTC 2018] org.broadinstitute.dropseqrna.barnyard.DigitalExpression SUMMARY=sample.coun…
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Dear Bcbio Team,
I upgraded bcbio recently to v1.1.5 and I am getting below error when running gatk-variant pipeline.
[April 28, 2019 10:11:25 AM AST] org.broadinstitute.hellbender.tools.spark.A…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/compbiomed/animalcules
Confirm the following by e…
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Dear Silas,
Last time, I consulted you about the taxonomic and functional profiling for metagenomic data. After check the several papers and blocks, I want to try metaphlan2 and humann2 to get taxo…
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Hi, thanks for creating this amazing tool for decontamination
We are working with low biomass samples, and we have some questions:
1) in our case, the real features in our library will be probably v…
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I'm not sure if this is the best place to start, but I've been following the conversation on BioJulia/Phylogenies.jl#1 and I thought it might be worth starting a conversation (inspired by @mkborregaar…
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I am little confused by counting the abundance of species in metagenomics-wide sequencing. If we used the read counts as the abundance of the species, shall we normalize it. Liking the RNA-seq, maybe …
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### Expected behavior
Taxonomic classification with sourmash and kaiju using the command ./run_all.sh
### Actual behavior
The kaiju database downloading step is finishing with an error
Downl…