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Continued with issue #404, I found that some pdb files don't have ATOM records at all in high quality ESM atlas. (I haven't checked full database.)
e.g.,
highquality_clust30_00.tar
./403/MGYP000179…
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Hi Anamaria,
I would like to suggest you to incorporate also the work on codon usage bias and its linkage to growth rate in genomic/metagenomic data as introduced in Vieira-Silva & Rocha (https://jou…
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Currently the mbio upload form allows biom files only. @dpbisme mentioned this is not ideal, because biom files are tough to make for the general user. Users are much more likely to have tsv files: on…
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apcamargo
Hi,
First of all, thank you for you excellent tools, i did some test on my virus metagenomic data by prodigal-gv and prodigal 2.6.3 in " p meta", and i finally get 2440739 proteins by pro…
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Thank you very much for your great work.
We are going to perform metagenomic analyses by 16S using human tissue samples. I would like to make sure about "DNA quantitation data". Is this "pre-PCR co…
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Identify all (meta)genomic datasets that meet certain environmental measurement thresholds (e.g. all samples at X°C, with Y nitrate concentration, Z phosphate concentration)
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Hello, I am trying to run Opera-MS on the test dataset and have run into an error about Gapfilling and Mummer. To troubleshoot, I removed the "> /dev/null 2> /dev/null" line in "run_mummer_large_ref.p…
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Montana correctly pointed out in [this comment](https://github.com/microbiomedata/issues/issues/413#issuecomment-2067398721) that our implementation of long-read metagenomics was somewhat incomplete. …
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Hi,
I'm wondering is there any way to access the taxonomic data that STAT is automatically generating on each NCBI run? Every metagenomic upload on the SRA has this analysis generated and displayed a…
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Are we suppose to compile this data ourselves? fetch_ena.py seems to generate this data, but fetch_ncbi.py does not.