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Hi Atul,
In response to your email of yesterday. I weird, it works on your computer… Yes, I used ‘python3’ and bowtie ‘v1’.
As troubleshooting, I try some things.
(1) Build the index by mysel…
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Hi,
I found that gffread (v0.12.7.) can not deal with large chromosomes, we may find minus coordinates when using gffread to deal with such large chromosomes, for example, for a genome here https:/…
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Occasionally, the next genome will register as the end-state of the previous genome instantly. Might have the game reset, take a screenshot, pause, then reset again.
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Hi
kblin,
Meeting error when run following: ncbi-genome-download --species-taxids my_taxids.txt bacteria --formats fasta
ERROR: Download from NCBI failed: ConnectionError(MaxRetryError("HTTP…
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I'm curious if this process works when one maps the reads to a reference genome for another species. For example, we have low-coverage reads (``14x) for one species and have inferred a reference-based…
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It looks like the summary report may be reporting wrong genome sizes.
For human (taxID 9606):
From report: 6,339,524,059 (2X bigger than expected)
From [NCBI](http://www.ncbi.nlm.nih.gov/genome?LinkN…
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One last question: when I download the reference genome at home I have no problems, but here at work we have a very restricted internet using a proxy and the download doesn't work. Could you tell me t…
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Lets decide how we go with this.
I think it makes sense to test current assembly with real data that needs analysis to gauge status.
I sugget two ways forward -
More PacBio or Nanopore....
sr320 updated
6 years ago
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https://doi.org/10.1038/s41586-024-07769-3
Please keep this checklist for curation of a new study.
- [ ] [create an issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before cur…
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Hi,
I'm using a lot panaroo for a research project. I generated a gene_presence_absence matrix from 1500 bacterial genomes.
Then I used this matrix to train a supervised machine learning model. I go…