Visualization of maf alignments in JBrowse

Question

[ifreecell]

I have set up a local JBrowse, and very satisfied with it. However, I could not find info about how to set up a UCSC Genome Browser-like Conservation track, which is a great feature for comparative analysis. Is there any way (plugin) to visualize Multiz Alignments in JBrowse? If so, how to format the data?

[GenoMax]

Was not possible a year ago based on this response. But that may have changed since.

[Bioinformatics_NewComer]

Hi,

Not to be harsh, but it might be worth picking JBrowse developers' brain on their highly active mailing list. :)

Answer 1

[cmdcolin]

I have created something like this using a jbrowse plugin https://github.com/cmdcolin/mafviewer

Update: added some optimizations, did some sanity checking, tested on 99 vertebrate alignments

Feel free to give it a try and provide feedback! Note: my original answer linked to multibigwig plugin

[SES]

This looks really nice. Also, if you don't mind sharing, what glyph/configuration are you using for your genes track?

[cmdcolin]

Those are just standard genes from a gff loaded as a CanvasFeatures track, no extra configuration other than loading flatfile-to-json with --trackType CanvasFeatures :)

[SES]

Thanks for the response! I don't think I used the --trackType CanvasFeatures option which may be why my genes are showing up as a grey span with no subfeatures. I'll try it.

[cmdcolin]

No worries. There are a lot of options when it comes to loading and customizing the tracks! I added a short FAQ entry about this http://gmod.org/wiki/JBrowse_FAQ#My_HTMLFeatures_don.27t_show_up_with_subfeatures.2C_why_not.3F

[SES]

That did exactly what I wanted! I'm so happy because I couldn't figure this out in my previous attempts. I did try to use the CanvasFeatures type in the main configuration but I must have skipped that part when generating the json files. Thank you!

Answer 2

[cmdcolin]

random update: I created a JBrowse 2 version of this plugin! it's basically the same as the jbrowse 1 version but I am interested in making it even more feature-ful and connected to synteny and other features in the future https://github.com/cmdcolin/jbrowse-plugin-mafviewer