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tanghaibao / jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics
BSD 2-Clause "Simplified" License
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converting mummer result coords file to blast file #689

Open xiaoguizz opened 1 month ago

xiaoguizz commented 1 month ago

Hello, Mr. Tang I want to perform collinearity analysis based on the mummer result coords file, in my opinion, this requires converting the coords file to a blast file, but I didn't convert it successfully when I used python -m jcvi.formats.coords blast, and I didn't find the relevant guidance in your wiki, I don't know how to implement the collinearity analysis based on mummer now. Thank you very much for your reply!

tanghaibao commented 1 month ago

@xiaoguizz

Can you show what the error message was when converting from coords to blast file? thanks.

xiaoguizz commented 1 month ago

Hello, Mr. Tang, Thank you very much for your timely reply, the mummer transformation problem has been solved, but I don't know how to perform JCVI collinearity analysis based on coords results, do you have any good solutions here?

Adamtaranto commented 1 month ago

@xiaoguizz Can you please post your solution here, it may help future users.

Are you trying to do the analysis using whole genome alignments?

xiaoguizz commented 1 month ago

Yes, I have now generated the coords file and I want to use JCVI to de-collinearity plots.

wangchengww commented 1 month ago

I have the same question as well. I want to conduct a genome synteny analysis using NUCmer. Could you advise on how to plot the multi-genome macrosynteny relationships?

tanghaibao commented 1 month ago

Most of the synteny generation and filtering within JCVI is centered around using 'markers' (or genes). While it is possible to carry out this analysis with NUCmer, it is currently unsupported and likely not going to work particularly well for large genomes without tuning the parameters against NUCmer.