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Questions tagged [pangenome]

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Calculating Fisher's exact test for COG categories

This is a continuation of the following question - Fisher's exact test for COG categories in pan, core genome analysis Also, the dataset - How do I perform a Fisher's exact test on this data to ...
K_081's user avatar
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1 vote
1 answer
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Fisher's exact test for COG categories in pan, core genome analysis

I have come across several papers that do a Fisher's exact test to show over represented genes in COG categories specifically in a pan-core-accessory-species specific genome analysis. The test is done ...
K_081's user avatar
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Current 'most comprehensive' whole genome alignment resource for human?

I found the human genome alignment sets here: https://www.ensembl.org/info/genome/compara/multiple_genome_alignments.html but they doesn't include, for example, ancient human genomes, e.g. those here: ...
Dan Bolser's user avatar
2 votes
2 answers
60 views

Error with eggNOG-mapper jobs

I recently tried using eggNOG-mapper for pan-genome and core genome analysis of files from OrthoFinder, specifically the 'Orthogroup_Sequences' which contains a huge list of protein files in fasta ...
K_081's user avatar
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1 vote
0 answers
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Constructing a pangenome graph using multiple samples

I am working with yeast strains (specifically S. cerevisiae) that have been cultured and evolved over many generations in the lab. I am using the reference S288C strain when I do certain analyses but ...
rimo's user avatar
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