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> For yeast, Ensembl works well:
unrelated, but where can I get your original FASTA and GFF3 files? Are you just grabbing most of them through here? https://uswest.ensembl.org/Saccharomyces_cerevi…
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For new term requests, please provide the following information:
## Preferred term label
taxon as collection of organisms
## Synonyms
taxon
## Textual definition
A collection of orga…
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The `adapter_removal` task terminates in an unexpected manner:
```
Error executing process > 'adapter_removal (COD092E1bL1i69_L7)'
Caused by:
Process `adapter_removal (COD092E1bL1i69_L7)` t…
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When I presented [the geoduck data at PAG 2020](https://github.com/shellytrigg/talk-pag2020), some people thought the BUSCO score of 71.5% (which our manuscript currently reports) was low, as was prev…
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Dear mbnmbn00,
Can we use FunGAP for plant genome annotaion?
The second query is when the speceis is not available in augustus and it shows the following error
"We did not find any augustus species…
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To infer organisms form the fastQ samples, the top most over-represented organisms in [SRA](https://www.ncbi.nlm.nih.gov/sra) are being selected based on the following parameters:
- Fraction of sam…
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Hi Bergman Lab folks,
Thanks for developing McClintock! I'm in the process of testing it for us in my research. While I'm finding it useful, it also looks like RelocaTE is prohibitively slow for mo…
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Hey there,
Is there a common way to remove false positives which are introduced by LTR-Harvest? I was following this protocol (http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library…
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Program works fine with Gencode but not Ensemble? How do I get it to work?
**Steps to reproduce**
- wget ftp://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.gtf.gz
- mkd…
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Post-lab meeting - swap out using a segment of the _Chlamydomonas_ genome for a region from _D. melanogaster_, and use mutation matrix from Chan et al 2012. See #16 for original issue.