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For #133 we use SRA as one of our sources. Optimizing our license for re-use would be greatly aided by having a summarized grade for NCBI's SRA.
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I thought I was missing some metadata in one of our own previously-submitted SRA datasets because it wasn't showing up in the CSV file, but then the SRA admins pointed out that it *does* show up on th…
ressy updated
5 years ago
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I am writing to seek your assistance with a question regarding the Cloud-based Taxonomy Analysis Information Table.
I noticed a discrepancy between the “identified_spot_count” available on the clou…
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I was able to install this program.
However, It is hard to figure out which script/binary need to run first?
For example, do we need to download the list of taxonomy IDS in order to build an ind…
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All of the SRA tests have been skipping because of a failure to download the necessary SRA drivers.
This started happening sometime between september 20th and october 24.
It looks like there w…
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Following my previous issue - I still don't get the fastq files with aspera, only empty folders, with the following code:
```
from pysradb.sraweb import SRAweb
SRA_OUR_DIR = "/data/NCBI_data/"
d…
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# OGS remapping and manual annotations
- [ ] request whole-genome alignment
- [ ] Set up data directories and get data
- [ ] run remap-gff3
# Change old content
- [ ] back up and deprecate ol…
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## Expected Behavior
the workflow should install the Conda packages before submitting the parallel steps.
## Actual Behavior
Running a workflow with `--no-container --beta-conda-dependencies ` an…
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Would it be possible to do a parallelized `sra` and `fastq-dump` on multiple samples? I'm downloading this [~2k sample dataset](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585) on our super…
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Hey there, Lucas.
Thank you for this amazing tool.
I'm running grenedalf v-0.6.0. I've been able to use its 'diversity' and 'fst' functions, but for some reason I am getting a 'Segmentation Faul…