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schneebergerlab / plotsr

Tool to plot synteny and structural rearrangements between genomes
MIT License
282 stars 28 forks source link

alternative for syri #85

Open onbio opened 1 month ago

onbio commented 1 month ago

Hi,

I wanted to know if you tested this tool with any other software than "syri". I tried a ton of things to run syri, but did not succeed. It would be great if a less dramatic tool could do the work. It would be better to start with something you have tested than to jump on to another tool and encounter another issue.

Thanks in advance for your help.

mnshgl0110 commented 1 month ago

Plotsr also accepts input in BEDPE format (example), this is described here. If there is any specific error message or bug then please share that, otherwise it is difficult to understand what is the problem.

onbio commented 1 month ago

Thanks Manish for your quick response,

My apologies for not making myself clear. I could not install the syri tool required at Step 2( for Finding structural annotations between genomes). I tried different ways including the docker, nextflow, miniconda and manual installation, but I could not make the tool install. I am working with windows WSL (don't have the liberty to switch to linux). The docker installation somehow does not seem to work, I believe this is due to restrictions from my IT admin. Similarly, the conda installation had some dependency/core system file link issues. Thus It would be great if I could use another tool, that could generate the required BEDPE output using the minimap2 bam.