obtaining sequence via highlight-drag

[tcbishop]

at one website (lost the link) i was able to highlight a region of genome in IGV and download the sequence as a fasta file. I'd like to instead push that same fasta information directly to some tools I've developed.

How best to achieve this? Thanks

[jrobinso]

I assume you are asking about igv.js not IGV (desktop). I don't know what website you are referring to, this isn't currently possible with igv.js. In fact there is no way currently to "highlight a region" though the UI, although we will be adding that capability soon.

[jrobinso]

How did you accomplish this with Dalliance? Do you have a demo of it?

[tcbishop]

The yellow resizable slider bar appearing on dalliance at https://dna.engr.latech.edu/~gdash/GDash-min/ serves as our sequence selector in G-Dash.

A collaborator inserted  this functionality for us some years ago. How? IDK

Tom

On 4/29/22 2:07 PM, Jim Robinson wrote:

How did you accomplish this with Dalliance? Do you have a demo of it?

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv.js/issues/1500#issuecomment-1113636659, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA2KOH2CN7SZT3SZNLNXPE3VHQXO3ANCNFSM5UW2RU2A.https://dna.engr.latech.edu/~gdash/GDash-min/ You are receiving this because you authored the thread.Message ID: @.***>

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Thomas C. Bishop Hazel Stewart Garner Associate Professor Chemistry & Physics Tel: 318-257-5209 Web: dna.engr.latech.edu

Spring 2022 Office Hours: (also by appointment) MWF 10:00am-noon (EA 207) T/Th 1:00pm-3:00pm (Biomed 306)

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[tcbishop]

that would explain why I can no longer find the example. Turns out it was Jbrowse not igv.js . my apologies.

Tom

On 4/29/22 1:17 PM, Jim Robinson wrote:

I assume you are asking about igv.js not IGV (desktop). I don't know what website you are referring to, this isn't currently possible with igv.js. In fact there is no way currently to "highlight a region" though the UI, although we will be adding that capability soon.

— Reply to this email directly, view it on GitHub https://github.com/igvteam/igv.js/issues/1500#issuecomment-1113593548, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA2KOHYMF47N6QRLRWL7KUTVHQRUJANCNFSM5UW2RU2A. You are receiving this because you authored the thread.Message ID: @.***>

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Thomas C. Bishop Hazel Stewart Garner Associate Professor Chemistry & Physics Tel: 318-257-5209 Web: dna.engr.latech.edu

Spring 2022 Office Hours: (also by appointment) MWF 10:00am-noon (EA 207) T/Th 1:00pm-3:00pm (Biomed 306)

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[jrobinso]

This would be new functionality for igv.js. If you already have this working with JBrowse maybe that's a better choice. Unlike JBrowse igv.js does not have a plugin API.