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bhattlab / MGEfinder

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
MIT License
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Using MGEfinder with multiple species #31

Closed spencer411 closed 2 years ago

spencer411 commented 3 years ago

This is a question more than an issue. I am interested in looking for MGEs shared across multiple species of staph. In doing so, should I map all the reads with BWA to a single ref species (one which shares the most genes with all others), or do BWA mapping to the individual reference for each specie? I guess my question is are MGEs identified across different species using species specific reference species going to be comparable?

Thanks in advance for your input!

durrantmm commented 3 years ago

Hello!

Thank you for your question. I would choose one representative genome for each Staph species. The MGEs should be comparable to each other, you can align them all to each other across your different genomes and cluster them. It will be more difficult to compare integration sites, but not impossible! Happy to talk more about that if you're interested.

Best, Matt Durrant

From: spencer411 @.> Sent: Monday, October 4, 2021 8:46 AM To: bhattlab/MGEfinder @.> Cc: Subscribed @.***> Subject: [bhattlab/MGEfinder] Using MGEfinder with multiple species (#31)

This is a question more than an issue. I am interested in looking for MGEs shared across multiple species of staph. In doing so, should I map all the reads with BWA to a single ref species (one which shares the most genes with all others), or do BWA mapping to the individual reference for each specie? I guess my question is are MGEs identified across different species using species specific reference species going to be comparable?

Thanks in advance for your input!

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