How to find the Insertion-Enriched Sites caused by Insertion sequences

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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How to find the Insertion-Enriched Sites caused by Insertion sequences #39

Closed Daikuang closed 2 years ago

Daikuang commented 2 years ago

Hi Matthew, I’m very interested in the Analysis of Insertion-Enriched Sites in your paper. I am trying to analyze Insertion-Enriched Sites caused by Insertion sequences (the upstream, within and downstream of the nearest CDS) among 200 complete sequenced bacteria. I wonder if I can use the MGEfinder tool to do this? If yes, Could you please give me some idea (or the workflow)? Many thanks in advance. Sincerely, Dai Kuang

durrantmm commented 2 years ago

Yes, it certainly could be used to do that. The wiki should help you get started with the MGEfinder command-line interface. This will identify insertions, but there is no software for automatically calculating which sites are enriched. I described how I did it in the paper.