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cmdcolin / jbrowse-plugin-mafviewer

A viewer for multiple alignment format (MAF) files in JBrowse 2
Apache License 2.0
9 stars 0 forks source link

Long alignment didn't work #7

Open baozg opened 6 months ago

baozg commented 6 months ago

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

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cmdcolin commented 6 months ago

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 commented 6 months ago

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

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cmdcolin commented 6 months ago

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 commented 6 months ago

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.

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cmdcolin commented 6 months ago

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