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Copy and paste the exact command I tried to run:
`flair collapse -r test_input/reads.fa -q test_input/test.corrected.bed -g test_input/genome.fa -t 4 --longshot_vcf test_input/longshot.vcf --longsho…
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Hi egaffo, thanks for the prompt reply. I tried the new docker but I keep having a similar error:
user@NGS:~/CirComPara$ sudo docker run -u `id -u` --rm -it -v $(pwd):/data egaffo/circompara2:v0.…
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Hello,
I'm running into an error at the Deseq2 step, this is the error given deseq2.Rout:
```
./improve_deseq_table.rb:25:in `block in ': undefined method `[]' for nil:NilClass (NoMethodError)…
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### Your idea
### EDIT
github draft for current discussion: https://github.com/PESTILLILAB/bids-specification/blob/bep038/src/atlas.md
the google doc draft (deprecated in favor of the github dr…
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Hello, I am curating 10X single-cell data for repertoire loading into iReceptor and I have a question about metadata annotation.
Regarding the cell_phenotype field, I am wondering how to represent…
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**Describe the bug**
Receiving a 504 error when submitting request to load RNA-seq data with the TPM data type.
**Link to page(s) where bug is occurring**
https://seqr.broadinstitute.org/data_man…
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@NathanSkene @KittyMurphy @Al-Murphy
While I was waiting for the latest phenotype-celltype enrichment results to finish running on HPC, I starting exploring whether we could run phenotype-celltyp…
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Dear Professor:
I found through literature review that HaMStR can identify orthologous clusters from genomes or transcriptomes(http://www.deep-phylogeny.org/hamstr/) by performed with strict p…
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Currently, we curate COB using COB ids, and swap out COB ids with exact matches (e.g. COB:cell nucleus with GO:cell nucleus).
This is cumbersome for a variety of reasons:
1. It is unclear who ow…
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Currently the input/output files are a bit of all over the place. We need to came up with a plan that sensiblely sorts them out.
Expectation:
- [ ] ETL output data.
- [ ] ETL input files produced…