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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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Unequal number of chromosomes in the genomes #142

Closed diego-rt closed 2 years ago

diego-rt commented 2 years ago

Hello,

Is there a way to have syri process genomes with different numbers of chromosomes? In my case, I basically have 4 "genomes" with a single chromosome, and one in which that single sequence rearranged into 4. When I follow the "Pipeline for visualising genomic differences" section on the plotsr page, I get the following error with syri: Reading Coords - ERROR - Unequal number of chromosomes in the genomes. Exiting.

Would be super cool if I could plot this using syri / plotsr!

Thanks and congrats on the cool program!

mnshgl0110 commented 2 years ago

Syri expects same karyotype across genomes. So, by default, this case cannot be handled. But you can merge the 4 rearranged sequences to get 1 pseduochromosome and then you can analyse them normally. In the plotsr visualisation, you can add markers to point the positions where the sequences were merged. Though not-very elegant, but I think this may work.

diego-rt commented 2 years ago

I see, sounds like a good solution. Will try it. Thanks a lot!