Re: [Gmod-ajax] Jbrowse2 | Highlight parameter Issue

[Revanth S. K. R. P. <rpa...@un...>]

Hello Colin,

Thank you for the response!

Yes, I got it to work upgrading jbrowse version to the latest one.

Yeah, I think the feature to see where the current chromosome is located in entire genome would help for the researchers. Please let me know if you need any other information.

Thanks!


From: Colin <col...@gm...>
Sent: Thursday, November 21, 2024 3:05 PM
To: Revanth Sai Kumar Reddy Patel <rpa...@un...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] Jbrowse2 | Highlight parameter Issue

Caution: Non-NU Email

Hi there,

Here is an example of using the highlight parameter, I think it works. If it is not working, can you confirm your jbrowse version you are using?

https://jbrowse.org/code/jb2/main/?config=test_data/volvox/config.json&loc=ctgA:1-800&assembly=volvox&tracks=gff3tabix_genes&highlight=ctgA:100-700<https://urldefense.com/v3/__https:/jbrowse.org/code/jb2/main/?config=test_data*volvox*config.json&loc=ctgA:1-800&assembly=volvox&tracks=gff3tabix_genes&highlight=ctgA:100-700__;Ly8!!PvXuogZ4sRB2p-tU!ERa2mmwoCtuCjJJ0y-est3ou8y_QnuKyzNbELzELXeZVzz_Ew8imG9jUTmbspzPycnMtnPFRSwJseZM-p7Bogw$>

>Another issue is when I load fasta assembly in jbrowse and in the search if I go to a specific gene or chromosome, I am losing the information of other genes to its sides as it only shows the gene searched for. Please let me know if there is a fix for this.

currently the search makes it zoom in to the exact boundaries of the feature of interest. do you want it to be a little more zoomed out? this is not currently configurable but we could try to add that


-Colin

On Wed, Nov 20, 2024 at 1:25 PM Revanth Sai Kumar Reddy Patel via Gmod-ajax <gmo...@li...<mailto:gmo...@li...>> wrote:
Dear Team,

Hope you are doing well. I appreciate the development and contributions to open source community for Jbrowse.

I am currently facing issue using highlight in URL, I am using it as suggested in the document, but I don’t see anything highlighted on the UI. Please help me what could be going wrong here, do I need to install any other plugins or change configs?

Another issue is when I load fasta assembly in jbrowse and in the search if I go to a specific gene or chromosome, I am losing the information of other genes to its sides as it only shows the gene searched for. Please let me know if there is a fix for this.

I appreciate your response.

Best,
[cid:image001.gif@01DB3C27.4AFAC0A0]
Revanth Sai Kumar Reddy Patel
Software/System Engineer – Dr. Yin’s Lab
University of Nebraska–Lincoln



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