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schneebergerlab / plotsr

Tool to plot synteny and structural rearrangements between genomes
MIT License
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Getting exact coordinates in an inversion/insertion region in a chromosome #36

Closed LandiMi2 closed 1 year ago

LandiMi2 commented 1 year ago

Hey folks! This is such a lovely tool for comparative genomics!! I am trying to get coordinates of where I have an insertion in one chromosome (reference) and not in the query. How can I extract the exact coordinates where I visualize this insertion towards the end? I am interested in the inversion coordinates too. Here is the plot Screenshot 2022-12-23 at 13 29 57

mnshgl0110 commented 1 year ago

Hi Michael, you can get the coordinates from the syri's output file (syri.out and syri.vcf). Also, insertion in one chromosome (reference) and not in the query is defined as a deletion (DEL) in syri's output.

LandiMi2 commented 1 year ago

@mnshgl0110 thanks! I will closely look at it. Do you have any documentation to syri's outputs?

LandiMi2 commented 1 year ago

@mnshgl0110 I also don't understand this error message when running plotsr Screenshot 2022-12-23 at 15 44 59

mnshgl0110 commented 1 year ago

syri documentation: https://schneebergerlab.github.io/syri/

regarding the error: I guess there would be some issue in the genomes.txt file. Make sure that it has correct file format. Specifically, ensure that the columns are separated by tabs and not spaces.

LandiMi2 commented 1 year ago

Aha, tabs, not gaps, yes, yes. Mine needed to be fixed with how I named the file (with no dots but maybe underscore uppercase and lowercase). For some reason, naming your file with the dots tab doesn't work. It works after a space, then a tab. Stupid me dint know this 😀

Thanks @mnshgl0110, for the quick responses!!!