Transcript sub parts with CanvasFeature

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Transcript sub parts with CanvasFeature

Henry
Hello,

I am having some difficulties figuring out how to get the exons to display on top of an mRNA segment when using flatfile-to-json.pl with CanvasFeature.

If I specify a type with the --type parameter, I get segments of only that type (mRNA, exon, CDS, etc). If I don't specify a type then every segment is loaded but each segment (mRNA, exon, CDS) is its own individual segment separate from every other segment.

How can I load a sequence with CanvasFeature so that the exons display on top of the mRNA segment?

Thanks for your time.

Henry




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Re: Transcript sub parts with CanvasFeature

Colin
Hello,
You might need to double check that the Parent/Feature relationship is made correctly. It needs to have "ID=parent" for a parent feature for example, and then "ID=subfeature;Parent=parent" for a sub feature (and yes, case sensitivity matters for this, so "Parent" and not "PARENT" -- that issue has cropped up fairly frequently).

Also, note that WebApollo is primarily made for working with HTMLFeatures tracks, because the CanvasFeatures are not yet "draggable" or "selectable" or enabled for the "edge-matching" feature. So, I would definitely try and see if HTMLFeatures would suit you needs better (but the parent child relationships should still be double checked)

-Colin


On Fri, Aug 7, 2015 at 9:57 AM, Nathan Henry <[hidden email]> wrote:
Hello,

I am having some difficulties figuring out how to get the exons to display on top of an mRNA segment when using flatfile-to-json.pl with CanvasFeature.

If I specify a type with the --type parameter, I get segments of only that type (mRNA, exon, CDS, etc). If I don't specify a type then every segment is loaded but each segment (mRNA, exon, CDS) is its own individual segment separate from every other segment.

How can I load a sequence with CanvasFeature so that the exons display on top of the mRNA segment?

Thanks for your time.

Henry




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Re: Transcript sub parts with CanvasFeature

Henry
The Parent - Child relationship was the problem. I had it formatted incorrectly.

Thanks for your help!

On Fri, Aug 7, 2015 at 12:00 PM, Colin <[hidden email]> wrote:
Hello,
You might need to double check that the Parent/Feature relationship is made correctly. It needs to have "ID=parent" for a parent feature for example, and then "ID=subfeature;Parent=parent" for a sub feature (and yes, case sensitivity matters for this, so "Parent" and not "PARENT" -- that issue has cropped up fairly frequently).

Also, note that WebApollo is primarily made for working with HTMLFeatures tracks, because the CanvasFeatures are not yet "draggable" or "selectable" or enabled for the "edge-matching" feature. So, I would definitely try and see if HTMLFeatures would suit you needs better (but the parent child relationships should still be double checked)

-Colin


On Fri, Aug 7, 2015 at 9:57 AM, Nathan Henry <[hidden email]> wrote:
Hello,

I am having some difficulties figuring out how to get the exons to display on top of an mRNA segment when using flatfile-to-json.pl with CanvasFeature.

If I specify a type with the --type parameter, I get segments of only that type (mRNA, exon, CDS, etc). If I don't specify a type then every segment is loaded but each segment (mRNA, exon, CDS) is its own individual segment separate from every other segment.

How can I load a sequence with CanvasFeature so that the exons display on top of the mRNA segment?

Thanks for your time.

Henry




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: Transcript sub parts with CanvasFeature

Colin
Glad to hear! Let us know if there is anything else that we can help with.


-Colin

On Mon, Aug 24, 2015 at 1:27 PM, Nathan Henry <[hidden email]> wrote:
The Parent - Child relationship was the problem. I had it formatted incorrectly.

Thanks for your help!

On Fri, Aug 7, 2015 at 12:00 PM, Colin <[hidden email]> wrote:
Hello,
You might need to double check that the Parent/Feature relationship is made correctly. It needs to have "ID=parent" for a parent feature for example, and then "ID=subfeature;Parent=parent" for a sub feature (and yes, case sensitivity matters for this, so "Parent" and not "PARENT" -- that issue has cropped up fairly frequently).

Also, note that WebApollo is primarily made for working with HTMLFeatures tracks, because the CanvasFeatures are not yet "draggable" or "selectable" or enabled for the "edge-matching" feature. So, I would definitely try and see if HTMLFeatures would suit you needs better (but the parent child relationships should still be double checked)

-Colin


On Fri, Aug 7, 2015 at 9:57 AM, Nathan Henry <[hidden email]> wrote:
Hello,

I am having some difficulties figuring out how to get the exons to display on top of an mRNA segment when using flatfile-to-json.pl with CanvasFeature.

If I specify a type with the --type parameter, I get segments of only that type (mRNA, exon, CDS, etc). If I don't specify a type then every segment is loaded but each segment (mRNA, exon, CDS) is its own individual segment separate from every other segment.

How can I load a sequence with CanvasFeature so that the exons display on top of the mRNA segment?

Thanks for your time.

Henry




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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