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The MiAIRR SRA element field for Sequencing Platform is not right, its example is for an instrument model and the Sequencing Platform should have a short list (about 8) of the platforms in a checklist…
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In publishing the latest versions of the 0x Python packages, we're migrating from v4 to v5 of Web3.py. v5 will not accept any non-checksummed addresses for any inputs to any contracts.
We have [an…
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Hi there,
I've been running SingleM on a set of SRA files. For most of them this is fast and takes < 10 minutes. Some SRAs, it seemingly runs forever and gets stuck. This is one example of such a …
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For all users, the standard has been to use the SRA toolkit. It would be great to have front-and-center documentation about how fusera differs, when fusera is preferred and why, and some use case tran…
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Hi, I'm installed parallel-fastq-dump on a cluster using SLURM, but i get this error:
(srr_download) moshea@moriah-gw-01:~$ parallel-fastq-dump --sra-id SRR2244401 --threads 4 --outdir . --split-f…
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on farm at `/home/ctbrown/scratch/2022-branchwater-benchmarking/wort-list-d.d/Snakefile` -
```python
# convert a bunch of .sig files into .sig.zip files and also produce .mf.csv fil
es.
FILELI…
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search at https://www.ncbi.nlm.nih.gov/sra/ for "METAGENOMIC"[Source] NOT amplicon[All Fields]
direct link courtesy of luiz:
https://www.ncbi.nlm.nih.gov/sra/?term=%22METAGENOMIC%22%5BSource%5D…
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Dear Brian
I am getting the following error message at the very last step of trinotate to write the annotation report. Would you mind helping me out?
I am running the exact codes you have avialabl…
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from: https://github.com/llvm/llvm-project/commit/8320b97ab9f25d726379832342f3d5d48962368d
to: https://github.com/llvm/llvm-project/commit/b5e47d2e409f2fb70c9397fccf4a74660c319bb0
commit: af7aab9c6040…
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this rule:
```
# download SRA IDs.
rule wc_download_sra:
output:
r1 = protected(outdir + "/raw/{sra_id}_1.fastq.gz"),
r2 = protected(outdir + "/raw/{sra_id}_2.fastq.gz"),
…