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Hello, professor
We got the uploaded halictids.params file, which displayed the cds file path for every species. I am trying to use the script selection_pipeline.py to filter my orthogroups fgenerate…
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I'm just wondering, what is the Orthogroup column in `N*.tsv` mean? I think the distinct orthogroups should be the HOGs, but sometimes I see that different rows will have the same Orthogroup ID, and I…
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Next step, I think, is to try to annotate the orthogroups from the Phaeo transcriptome/genomes ...
_Originally posted by @maggimars in https://github.com/maggimars/Tara-Phaeo/issues/4#issuecomment-…
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Bonjour,
J'ai un problème à l'étape Orthogroup tool et je ne comprend pas le message d'erreur.
```
Traceback (most recent call last):
File "/w/galaxy/galaxy3/shed_tools/toolshed.g2.bx.psu.e…
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I looked into this issue raised by @janfassler. My analysis and discussion can be read [here](https://htmlpreview.github.io/?https://github.com/binhe-lab/C037-Cand-auris-adhesin/blob/master/01-global-…
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In many of my Orthogroup sequence files, within the same orthogroup I am getting duplicate copies of the same exact gene, with identical identifiers and amino acid sequences. My original fasta files t…
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Hello David,
I encountered the following issue while running OrthoFinder: "ERROR: Species tree inference failed."
The command I used is: orthofinder -f ./data -t 24 -a 10 -M msa -S diamond -A m…
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Hello,
I'm having the following error when running genespace:
> out 8 unique places
...Carve_hap2: 2407 genes in 105 OGs hit > 8 unique places ***
NOTE! Genomes flagged *** have > 5% …
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See `/vortexfs1/omics/alexander/share/formaggi` for the genomic contigs, predicted coding sequences, and amino acid sequences :)
_Originally posted by @halexand in https://github.com/maggimars/Tar…
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Hello jtlovell,
Thanks for all your work on this package!
I'm using GENESPACE v1.3.1 in a conda environment with R 4.1.2 and have it successfully for your test dataset so it should all be worki…