GuilhemRoyer

I have found a way to do this but I am not sure I get all the spots: I search for my gene family in all the projection files and...

Thank you Adelme! In fact there is spot-related information in the projection files (column 13). So I was able to get the information but it was more tricky than the...

Thank you Adelme. Here is the command that I used: ppanggolin align -c 12 -p pangenome.h5 -o iroN_related_spots --sequences iroN.fasta --draw_related I can get a few spots, then it crashes...

Hi, I finally fix the problem by increasing the recursion limit of Python in the script "Ppanggolin/lib/python3.8/site-packages/scipy/cluster/hierarchy.py" """ import sys print(sys.getrecursionlimit(2500)) """ But, not sure if it is the best...

Hi andrenalina1, Glad you're using Plascope. I think your command is missing the "-a" option to specify the assembler. You should try the following command: plaScope.sh --fasta EC_mcr1.fasta -o ~/sep2023/genome/...

Ok, maybe there's a problem with the current version of PlaScope... We need to look into this further. Anyway, I'm pretty sure the problem is with your contig names. PlaScope...

Ok. Can you attach part of your fasta file (e.g, 2 or 3 contigs) so I can try modify it and send it back to you?

Sorry there was a mistake in my command line. Please try the following one on your fasta file : sed 's/>/>NODE_/g' [your_file.fasta] | sed 's/ length=/_length_/g' | sed 's/ depth=/_cov_/g'...

Hi, Currently Plascope can work only on SPAdes assemblies, but we plan to modify it. We prefer SPAdes assembly as we can get a deep coverage value from the header...

Hi J., Thanks for modifying the code and having proposed a version adapted to another assembler. Sure it will be great if you can do a pull request. Hope the...