Is there a way to extract a region of the reference sequence when zoomed out?

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Is there a way to extract a region of the reference sequence when zoomed out?

Monica Poelchau
Hi there,

One of our annotators would like to extract a particular region of the reference sequence using the 'save track data' option. This is possible in Web Apollo when zoomed in to base level, but if you zoom out, the reference sequence track disappears completely, including the label, so you can't access the 'save track data' menu option. Would it be possible to make the reference sequence track label visible at all zoom levels for annotators who need to extract particular sequence regions, or are there other ways to extract the reference sequence in a particular region in Web Apollo?

Thanks,

Monica
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Re: Is there a way to extract a region of the reference sequence when zoomed out?

nathandunn

In the client plugin or in the deployed root (jbrowse/plugins/WebApollo/js/View/Track/SequenceTrack.js), you can set ALWAYS_SHOW=true:

It won’t show the sequence, but the track won’t disappear and you can still choose “Save Track Data”. 

Nathan


On Oct 8, 2014, at 5:32 AM, Monica Poelchau <[hidden email]> wrote:

Hi there,

One of our annotators would like to extract a particular region of the reference sequence using the 'save track data' option. This is possible in Web Apollo when zoomed in to base level, but if you zoom out, the reference sequence track disappears completely, including the label, so you can't access the 'save track data' menu option. Would it be possible to make the reference sequence track label visible at all zoom levels for annotators who need to extract particular sequence regions, or are there other ways to extract the reference sequence in a particular region in Web Apollo?

Thanks,

Monica

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Re: Is there a way to extract a region of the reference sequence when zoomed out?

Monica Poelchau
Hi Nathan,

Thanks - it looks a little odd, but it works! 

Monica 

On Wed, Oct 8, 2014 at 9:01 AM, Nathan Dunn <[hidden email]> wrote:

In the client plugin or in the deployed root (jbrowse/plugins/WebApollo/js/View/Track/SequenceTrack.js), you can set ALWAYS_SHOW=true:

It won’t show the sequence, but the track won’t disappear and you can still choose “Save Track Data”. 

Nathan


On Oct 8, 2014, at 5:32 AM, Monica Poelchau <[hidden email]> wrote:

Hi there,

One of our annotators would like to extract a particular region of the reference sequence using the 'save track data' option. This is possible in Web Apollo when zoomed in to base level, but if you zoom out, the reference sequence track disappears completely, including the label, so you can't access the 'save track data' menu option. Would it be possible to make the reference sequence track label visible at all zoom levels for annotators who need to extract particular sequence regions, or are there other ways to extract the reference sequence in a particular region in Web Apollo?

Thanks,

Monica


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Re: Is there a way to extract a region of the reference sequence when zoomed out?

nathandunn

There may be a way to make the sequence show up when zoomed out, but I’m not sure what that is (or if that is even desired).  

Nathan

On Oct 8, 2014, at 6:19 AM, Monica Poelchau <[hidden email]> wrote:

Hi Nathan,

Thanks - it looks a little odd, but it works! 

Monica 

On Wed, Oct 8, 2014 at 9:01 AM, Nathan Dunn <[hidden email]> wrote:

In the client plugin or in the deployed root (jbrowse/plugins/WebApollo/js/View/Track/SequenceTrack.js), you can set ALWAYS_SHOW=true:

It won’t show the sequence, but the track won’t disappear and you can still choose “Save Track Data”. 

Nathan


On Oct 8, 2014, at 5:32 AM, Monica Poelchau <[hidden email]> wrote:

Hi there,

One of our annotators would like to extract a particular region of the reference sequence using the 'save track data' option. This is possible in Web Apollo when zoomed in to base level, but if you zoom out, the reference sequence track disappears completely, including the label, so you can't access the 'save track data' menu option. Would it be possible to make the reference sequence track label visible at all zoom levels for annotators who need to extract particular sequence regions, or are there other ways to extract the reference sequence in a particular region in Web Apollo?

Thanks,

Monica