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schneebergerlab / plotsr

Tool to plot synteny and structural rearrangements between genomes
MIT License
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Question about output #61

Closed mylena-s closed 1 year ago

mylena-s commented 1 year ago

Hi! Thanks again for the tools! I am using plotsr with syri output. I was wondering if there is any way to get the ids of the plotted rearrangements (since they are a subset of all SV detected by syri)?

Thanks!

mnshgl0110 commented 1 year ago

By default, plotsr plots rearrangements larger than 10kb (either on the reference or the query genome) (parameter -s). You can fetch such rearrangements from syri.out, re-format and parse them to plotsr as markers.txt. Unfortunately, this would require some scripting as there is no direct method to do this.