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Hi,
I have a question regarding the behavior of CAT. I have (will have, it's running) a 63 genome alignment and transcriptomic data for a minority of them (~7), the reference annotation seems to be…
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Hello! Hope you are all doing well! For the output alignments (nucleotide.fasta, codon.fasta, and protein.fasta), what gene projections/orthology classes are included here? By that I mean, what does T…
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### Issue: `ValueError: No objects to concatenate` during `motif_enrichment_dem` Execution
```bash
scenicplus grn_inference motif_enrichment_dem \
--region_set_folder /n/sci/SCI-004375-NYUDATA/…
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Hello, I'm running dNdS() on the cds of 2 species containing 13486 orthologous pairs, but only 1754 genes get the calculations done for. The rest runs into this error.
`ERROR: number of input seqs…
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Hi,
Thank you for developing this tool. I tried to run Scenic+ on my mutiome data and I got an error message that I don't quite understand.
Could you help me with this issue.
Thanks in advance
Thi…
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**Describe the bug**
Hello. I seem to be getting an error at the get_search_space step in the scenicplus pipeline with snakemake. Any immediate thoughts about why this could be? Should my region se…
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Hi Dr. @MichaelHiller
I have couple of queries regarding my TOGA outputs. I am working with vertebrates genomes (size ranging from 550Mb to 1Gb, all genomes that I considered are of very good qual…
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Hi! I hope all is going good!
I am trying to run gimme motif2factors (v0.17.1, installed through conda/mamba) on the genome of my organism to be able to run ANANSE. I set up a folder for a custom …
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Hi David,
I have run OrhoFinder `2.5.4` on the example data with the `-y` option and otherwise default parameters. The HOGs in the file `Phylogenetic_Hierarchical_Orthogroups/N0.tsv` for the orthog…
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Hello @JGASmits,
Although the dry run appears to have worked the real one did not.
Here is the log file:
(anansnake) iMac-Pro:anansnake pediatrics$ less Complete log: .snakemake/log/2023-08-3…