Long alignment didn't work

[baozg]

Hi, @cmdcolin

This plugin looks awesome! I am interested in presenting these variation from whole genome alignment for A.thaliana genomes.
maf2bed looks fine, but the jbrowser seems stuck for this long alignment. Do you have any idea about this?

Test on a M2 MacBook with Jbrowser 2.10.3

[cmdcolin]

the screenshot of the file you posted probably means you should use "MafTabixAdapter" and not "BigMafAdapter". I think if you changed that, it would fix the error you are seeing of "not a BigWig/BigBed file" (because the MafTabix files are indeed, not BigBed style format, it's tabix :)

[baozg]

Thanks for your prompt reply. Unfortunately, it throw another error.

[cmdcolin]

are you hand editing the configuration? Can you paste a copy of the config.json? and do you have the both the maftabix and the tabix index (.tbi)?

[baozg]

No, I didn't edit any config. When I also load the .tbi into Jbrowser2, the plugin seems to work. But I cannot see my query alignment (11C1). I can send you the genome and bed if you have time to check.

[cmdcolin]

that would work great, if you want to send it to me colin.diesh@gmail.com I can check it out

[cmdcolin]

This is perhaps late in the game but if you try the pggb or minigraph-cactus pipelines, it can generate some "jbrowse ready" MAF files. it also generates multi-sample VCF which can be viewed 2with the new multi sample vcf view modes https://jbrowse.org/jb2/blog/2025/04/18/v3.3.0-release/

I am also trying to brainstorm more ways to handle stuff like this but hope that helps