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I have just installed Hybpiper2 and I am running through the tutorial data. It seemed to install fine, and check_dependencies finds all of the dependencies. However, the assemble stage fails at the ex…
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For making complexes, we can sometimes make a call based on HTP expression studies that one may be the "ubiquitiously" expressed complex and the testis-specific.
Can we formalize this to make an F…
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First round of QC on the newly GOC generated human->mouse GAF file via orthology: https://drive.google.com/drive/folders/1uICd7pxqre6hwtKNnMV5NKTPfcgR9xGy
96K matches between new GOC file and MGI gen…
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I ran ggcaller on 66 capsular loci extracted from references. The first base is the first base of the first gene, and the last base is the last base of the last gene.
ggcaller --refs db_fasta.txt -…
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**Dear Panaroo software development team and community,**
I am reaching out with some questions regarding the use of Panaroo that have arisen during my research. Your insights or thoughts on these …
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I am trying to run four E. coli assemblies through the pipeline. The annotation was done with PGAP, so I use the "--remove-invalid-genes" flag. It seems like all gff3 files get loaded properly but whe…
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I believe these two complexes are referring to the same thing:
id: GO:0031372
name: UBC13-MMS2 complex
def: "A heterodimeric ubiquitin conjugating enzyme complex that catalyzes assembly of K63-li…
sjm41 updated
6 months ago
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Hi, I want to use panaroo on reference genomes annotated with prokka, but I am facing an error.
These are the commands I tried:
```bash
panaroo -i /panaroo/*.gff -o results --clean-mode stric…
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Dear author
I am trying to use TOGA for gene annotation, I went through all the steps as presented in the GitHub and it is doing well even for the first test case in which I got the same output as pr…
txfc updated
8 months ago
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Hello,
I am having issue with the paralog_retriever command as it is not catching paralogs that are known to occur in some of my samples.
For some background, I have run HybPiper2 before on som…