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SionBayliss / PIRATE

A toolbox for pangenome analysis and threshold evaluation.
GNU General Public License v3.0
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Plasmid comparison #49

Closed jellila closed 3 years ago

jellila commented 3 years ago

Hello 🙂

I would like to ask you some help/suggestions please. I am trying to create an image (either with brig or cgview or circos) where three plasmids are compared. Every plasmid comes from a different strain and they have some differences. My idea was to create a sort of pan genome of the three plasmids as a reference, and then blast every plasmid around this pan genome, showing the genes are present in every single plasmid. I hope this makes sense! I use pirate to perform the analyses, but actually i don't really know how to go on. I don't think that the pan_sequences.fasta file is what I need (since it contains the same gene multiple times), but also the representative_sequences.ffn is not ideal (as it only has one representative per gene cluster, and if a plasmids have duplications I won't be able to show them). Would anyone please have any suggestions?

Thank oyu.

Laura

SionBayliss commented 3 years ago

Hi Laura,

PIRATE has already done the BLASTing for you, The presence/absence file (PIRATE.gene_families.tsv) should contain the relevant info.

All the best, Sion

jellila commented 3 years ago

Thanks Sion!

P.S. I love your jokes!!!

SionBayliss commented 3 years ago

Thanks!

Feel free to suggest some for the next release :)