[Gmod-ajax] Question about file formats for genome alignment visualization in JBrowse

[Veselina K. <ves...@ya...>]

Hello, JBrowse team,
My name is Veselina!
I would like to ask you a question regarding sequence alignments viewed in JBrowse.I use the downloaded app on my computer to visualize genomes and map reads. I also want to visualize 2 aligned genomes. I did the alignment in Galaxy platform using the mauveprogressive tool that generated an xmfa file. Can you please advice me on how I can view this alignment. I am not sure how to convert the xmfa file to suitable for visualization format. I can convert this file to GFF3 file using Galaxy as well, but I see this is not working in the visualization as well.
Additionally, I use windows 11 system that is very limited in bioinformatics. I tried to install pybigwig using python but it didn't worked out. Also I am not an bioinformatician, so any help that is provided for a wet-lab person would be highly appreciated.
May be I can use another aligner for my genomes (6.8 M bp large) that will create suitable file formats. If so, please advice.
Thank you endlessly for the time!
Have a good day!

Regards,


 
VeselinaPanova
Researchstudent at GSB, Kyoto University
  ves...@ya...|pan...@st...



  080-3135-8831
  https://www.lif.kyoto-u.ac.jp/e/research/lab/137/