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I have tried running scaffold a few times on a sample, and I keep getting an error. The details are below.
During scaffold, the following command failed with return code -11:
> > /opt/metAMOS/metAM…
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## Friday, October 12
### Project Background
#### Prior Sample/Data Processing
* Samples collected from marine environments around the world
* Water sample collected
* Filtered to isolate vir…
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Hey @allind
I tried to install eukdetect but when I run this command:
conda env update --name Eukdetect -f environment.yml
it gave an error saying:
SpecNotFound: Invalid name, try the format: us…
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Hi,
I am quite new to microbiome analysis and, frankly, quite at a loss as to how to proceed. So, I apologize is my question is naive or has already been answered elsewhere. I have just read a paper …
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@wdduncan @lwaldron @lgeistlinger @cmungall
From our conversation on Thursday (thank you btw @wdduncan, it was really helpful), we discussed how to structure the relationship between the microbiome…
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**Submitting author:** @wsmets (Wenke Smets)
**Repository:** https://github.com/LebeerLab/tidytacos
**Branch with paper.md** (empty if default branch): master
**Version:** v0.3.0
**Editor:** @diazrena…
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I've been working on several data sets lately looking at community change before/after a treatment, and have been working on [some code](https://gist.github.com/gregcaporaso/79dc526708b1e739ea8d) for …
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Links to metaproteomic public repositories
IDEA:
It would be a good idea to add a few common publically available metaproteomics databases (see HOMD database for an example below) to the Protein…
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## Tasks
1. all PCGs BLAST all-vs-all search - diamond.py
2. gene sets construction
3. real alignments to respective sample contigs specific to gene coordinates
4. module detection of coverage-c…
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Thanks for posting this public rebuttal! Good science is open science.
There's been some suggestion that removing environmental contaminants, as done in the original paper, removes the cancer sub-t…