Comments (1)
gtonkinhill
commented on September 8, 2024
Hi @luhan125 ,
From your earlier post it looks like you are running Panaroo on metagenomic data. It was not designed for this so if that is the case I would recommend using a different tool.
The gene names in panaroo include all gene names in each cluster separated by a ~~~.
Please refrain from posting questions on other users issues as this creates confusion.
I am afraid I am unable to answer so many questions about how to interpret the output of pangenome software. I will do my best but it might be better to read the documentation and some background material carefully before posting additional questions.
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Related Issues (20)
- Query Regarding Discrepancy in Output Information for Dataset of 3245 GFF3 Files HOT 2
- Request for Assistance in Identifying Core Genome from Result Files HOT 2
- Panaroo run time HOT 4
- Recovering gene coordinates HOT 2
- What to do with "xx_refound_yy" items in gene matrix?
- Gene sequences alignment HOT 2
- Gene clusters annotation HOT 1
- Invalid file extension HOT 1
- Not running with prokka generated gff files HOT 4
- provide separate gff and fasta files as input for panaroo HOT 2
- "NameError: Duplicate entry!!!" with a specific GenBank genome HOT 1
- Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour? HOT 9
- Default CD-HIT length different percent different than displayed in help message HOT 2
- Biopython deprecation error HOT 2
- Get Multifasta or alignment for each CDSs HOT 1
- Potential bug in panaroo HOT 1
- How to find paralog gene sequence in pan_genome_reference.fa? HOT 2
- Update the gene name in results of panaroo by bakta HOT 1
- Add functionality to batch gene alignments HOT 2
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