pirovc / grimer Goto Github PK

Hi, thanks for developing a nice tool!
I wonder if you have the species or genera names of all the proposed contaminants you detected from your meta-analysis (contaminants.yml)?
Regards

"Hey, thank you very much for this cool tool. I'm working on amplicon sequencing derived from public data with taxa at the genus level. According to the instructions, the only mandatory input is the abundance table. However, I'm interested in finding contamination associated with this data. My idea is to use the contaminants reference, as my dataset doesn't have any controls. If I run the following command, the decontamination step is not performed:

grimer -i fungi.genus.raw.csv --transpose -f ","

Since my table is at the genus level and the contaminants.yaml contains NCBI accessions, how can I perform decontamination?

Thanks in advance,
Ailton."

Hi, I'm wondering if you can help me.
I am trying to install grimer as a conda environment on my local university cluster using mamba.
Initially I had a problem with the version of R, so created an environment first with the required R=4.0
However, I am still getting this message:
The following package could not be installed └─ grimer is uninstallable because it requires └─ biom-format >=2.1.10 , which conflicts with any installable versions previously reported.
I'm not sure how to resolve this issue, as I have biom-format installed, and all dependencies such as h5py are installed and up to date.

It is perfectly possible that I am doing something stupid or missing an important step.
Looking forward to trying this tool out, and would be grateful for any pointers on how to resolve this issue.

Kind regards,
Richard

Hi again,
I have a mock community I'm running through with my other samples, but I'm a little unsure how to specify this in the config file.

I am able to point to the mock sample by specifying the metadata value under 'sample-type' column, but I don't know how to direct grimer to the expected composition of the mock.
I have a tsv file which contains taxonomic levels for each mock member and expected relative frequency. Is it possible to also direct grimer to this data in the config file?
Thanks in advance.

Hi,
Thanks for this awesome tool!

I am studying some samples that might contain microbial and non-microbial eukaryotes. Samples are RNAseq PE and saved locally. Is there a way to run this pipeline to generate such a beautiful report?

Thanks,
—Mo