Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?

Question

[I0110]

I was wondering if there is a JBrowse/JBrowse2 track could show three colors for reads map to different nucleotide positions. I want to visualize Ribo-seq data which shows three nucleotide periodicity so I want to show the reads map to reading frame 0 as red, reading frame 1 as blue and reading frame 2 as green. Something like:

The data input should be something like:

The column should contain (1) read counts (2) chromosome (3) nucleotide position (4) strand (5) color (should have 4 options, if possible: red, blue, green and grey.) Thanks!!!

[cmdcolin]

hi there, I'm a jbrowse 2 dev. I haven't heard of this type of visualization. If you can tell me more about the format the data comes in I might be able to advise. for jbrowse 1 I made the mpileup plugin which might be a way to sort of generalize the "snp coverage" track...a similar thing may be able to be made for jbrowse 1 or 2 that could support riboseq https://github.com/cmdcolin/mpileupplugin

[I0110]

Thanks for your reply, I add the description for data input in the text.

[cmdcolin]

i did an initial assesment and it may be a bit tricky to add this to jbrowse 2 unfortunately. if you are patient in waiting, let me know and i can check into this more, might be a couple weeks or even months realistically though just given that i got a lot of other todos

[cmdcolin]

Actually...because i'm a people pleaser i did a bit more work and tried to make a demo of this usage as a jbrowse 2 plugin

See https://github.com/cmdcolin/jbrowse-plugin-riboseq

it might not be everything you need but i tried to follow the data format you gave

Let me know what you think. If you have more realistic data files, please email me at [e-mail] and i can review

[I0110]

Thanks a million! I have never used jbrowse2 but will give it a try.

[cmdcolin]

sure thing. there is a bit of a learning curve setting it up but let me know if you run into any problems. i generally recommend using the jbrowse 2 "web quickstart" https://jbrowse.org/jb2/docs/quickstart_web/

[cmdcolin]

also i am imagining that maybe you have an additional "coverage" wiggle file that goes along with the data you gave. if that's true let me know. i can brain storm, either you can modify your bedtabix to include the coverage info, or the jbrowse plugin can be modified to accept both the bed tabix and a bigwig of coverage info