Annotating ncRNAs

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Annotating ncRNAs

Kyle Tretina
Hi Ed,

Forgive me if this is a naive question, but what is the easiest way to annotate a non-coding RNA (i.e. rRNA/tRNA) in WebApollo? I have looked at the notes in the manual and am still having a lot of trouble with this.

Thanks,
Kyle

IGS
MMI
UMB
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Re: Annotating ncRNAs

Ed Lee
Hi Kyle,

The easiest (and currently only =) ) way to annotate ncRNAs (or any non-protein coding transcript) is to select the evidence from the static tracks, right click, select "Create new annotation", and then select the appropriate type.

Cheers,
Ed


On Thu, Mar 20, 2014 at 11:49 AM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

Forgive me if this is a naive question, but what is the easiest way to annotate a non-coding RNA (i.e. rRNA/tRNA) in WebApollo? I have looked at the notes in the manual and am still having a lot of trouble with this.

Thanks,
Kyle

IGS
MMI
UMB

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Re: Annotating ncRNAs

Kyle Tretina
Hi Ed,

When I right click a static track, the option to "Create new annotation" does not come up (see attached screen shot example). Am I misinterpreting what you mean?

Thanks,
Kyle


On Thu, Mar 20, 2014 at 4:11 PM, Ed Lee <[hidden email]> wrote:
Hi Kyle,

The easiest (and currently only =) ) way to annotate ncRNAs (or any non-protein coding transcript) is to select the evidence from the static tracks, right click, select "Create new annotation", and then select the appropriate type.

Cheers,
Ed


On Thu, Mar 20, 2014 at 11:49 AM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

Forgive me if this is a naive question, but what is the easiest way to annotate a non-coding RNA (i.e. rRNA/tRNA) in WebApollo? I have looked at the notes in the manual and am still having a lot of trouble with this.

Thanks,
Kyle

IGS
MMI
UMB



Screen Shot 2014-03-21 at 12.53.39 PM.png (119K) Download Attachment
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Re: Annotating ncRNAs

Ed Lee
Hi Kyle,

Are you running the latest version of WebApollo?  The ability to create annotations other than coding transcripts was added in the latest release (2013-11-22).

Cheers,
Ed


On Fri, Mar 21, 2014 at 9:54 AM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

When I right click a static track, the option to "Create new annotation" does not come up (see attached screen shot example). Am I misinterpreting what you mean?

Thanks,
Kyle


On Thu, Mar 20, 2014 at 4:11 PM, Ed Lee <[hidden email]> wrote:
Hi Kyle,

The easiest (and currently only =) ) way to annotate ncRNAs (or any non-protein coding transcript) is to select the evidence from the static tracks, right click, select "Create new annotation", and then select the appropriate type.

Cheers,
Ed


On Thu, Mar 20, 2014 at 11:49 AM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

Forgive me if this is a naive question, but what is the easiest way to annotate a non-coding RNA (i.e. rRNA/tRNA) in WebApollo? I have looked at the notes in the manual and am still having a lot of trouble with this.

Thanks,
Kyle

IGS
MMI
UMB



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Re: Annotating ncRNAs

Kyle Tretina
In reply to this post by Kyle Tretina
Hi Ed,

Thanks for the answer to the last question! I have noticed that if I drag a new gene model into the User-created Annotations, it does not automatically set longest ORF for that model, but will do so if the annotation is edited at all or if I set it manually. Is there a way to "Set Longest ORF" for all genes in the User-created Annotations track at once? This would be useful as a last-step precaution.

Thanks,
Kyle


On Thu, Mar 20, 2014 at 2:49 PM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

Forgive me if this is a naive question, but what is the easiest way to annotate a non-coding RNA (i.e. rRNA/tRNA) in WebApollo? I have looked at the notes in the manual and am still having a lot of trouble with this.

Thanks,
Kyle

IGS
MMI
UMB

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Re: Annotating ncRNAs

Ed Lee
Hi Kyle,

Do you have <use_cds_for_new_transcripts> set to true in your config.xml?  If so, it will use the evidence's CDS if available.  If you want to always calculate the longest ORF, set that value to false.

Cheers,
Ed


On Sun, Mar 30, 2014 at 9:06 AM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

Thanks for the answer to the last question! I have noticed that if I drag a new gene model into the User-created Annotations, it does not automatically set longest ORF for that model, but will do so if the annotation is edited at all or if I set it manually. Is there a way to "Set Longest ORF" for all genes in the User-created Annotations track at once? This would be useful as a last-step precaution.

Thanks,
Kyle


On Thu, Mar 20, 2014 at 2:49 PM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

Forgive me if this is a naive question, but what is the easiest way to annotate a non-coding RNA (i.e. rRNA/tRNA) in WebApollo? I have looked at the notes in the manual and am still having a lot of trouble with this.

Thanks,
Kyle

IGS
MMI
UMB


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Re: Annotating ncRNAs

Kyle Tretina
In reply to this post by Ed Lee
Hi Ed,

We just updated to the latest version of WebApollo, and I still don't see a "Create new annotation" option when I right click on the evidence in the static tracks (see attached screen shot) in order to make a non-coding RNA model. Am I misunderstanding what you meant?

Thanks,
Kyle


On Fri, Mar 21, 2014 at 4:04 PM, Ed Lee <[hidden email]> wrote:
Hi Kyle,

Are you running the latest version of WebApollo?  The ability to create annotations other than coding transcripts was added in the latest release (2013-11-22).

Cheers,
Ed


On Fri, Mar 21, 2014 at 9:54 AM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

When I right click a static track, the option to "Create new annotation" does not come up (see attached screen shot example). Am I misinterpreting what you mean?

Thanks,
Kyle


On Thu, Mar 20, 2014 at 4:11 PM, Ed Lee <[hidden email]> wrote:
Hi Kyle,

The easiest (and currently only =) ) way to annotate ncRNAs (or any non-protein coding transcript) is to select the evidence from the static tracks, right click, select "Create new annotation", and then select the appropriate type.

Cheers,
Ed


On Thu, Mar 20, 2014 at 11:49 AM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

Forgive me if this is a naive question, but what is the easiest way to annotate a non-coding RNA (i.e. rRNA/tRNA) in WebApollo? I have looked at the notes in the manual and am still having a lot of trouble with this.

Thanks,
Kyle

IGS
MMI
UMB





tRNAScan_pred.png (55K) Download Attachment
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Re: Annotating ncRNAs

Colin
Hi Kyle,
I think the issue is that you have to use the HTMLFeatures track type in order to get those right-click menu items (and Draggable behavior) instead of CanvasFeatures. Sorry about the confusion!
Maybe we'll get to add CanvasFeatures support in a later release

-Colin


On Fri, Apr 4, 2014 at 12:49 PM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

We just updated to the latest version of WebApollo, and I still don't see a "Create new annotation" option when I right click on the evidence in the static tracks (see attached screen shot) in order to make a non-coding RNA model. Am I misunderstanding what you meant?

Thanks,
Kyle


On Fri, Mar 21, 2014 at 4:04 PM, Ed Lee <[hidden email]> wrote:
Hi Kyle,

Are you running the latest version of WebApollo?  The ability to create annotations other than coding transcripts was added in the latest release (2013-11-22).

Cheers,
Ed


On Fri, Mar 21, 2014 at 9:54 AM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

When I right click a static track, the option to "Create new annotation" does not come up (see attached screen shot example). Am I misinterpreting what you mean?

Thanks,
Kyle


On Thu, Mar 20, 2014 at 4:11 PM, Ed Lee <[hidden email]> wrote:
Hi Kyle,

The easiest (and currently only =) ) way to annotate ncRNAs (or any non-protein coding transcript) is to select the evidence from the static tracks, right click, select "Create new annotation", and then select the appropriate type.

Cheers,
Ed


On Thu, Mar 20, 2014 at 11:49 AM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

Forgive me if this is a naive question, but what is the easiest way to annotate a non-coding RNA (i.e. rRNA/tRNA) in WebApollo? I have looked at the notes in the manual and am still having a lot of trouble with this.

Thanks,
Kyle

IGS
MMI
UMB





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Re: Annotating ncRNAs

Kyle Tretina
Hi Colin,

The HTMLFeatures track was loaded with this command:
# ./bin/flatfile-to-json.pl --gff data/B_microti_4_chrom_plus_mito.tRNAscan-SE.gff3 --trackLabel "tRNAscan preds" --trackType HTMLFeatures

I could then see the "Create new annotation" option, but when I added the tRNA, I got the attached error message. Any ideas on what we need to change?

Thanks,
Kyle



On Fri, Apr 4, 2014 at 1:59 PM, Colin <[hidden email]> wrote:
Hi Kyle,
I think the issue is that you have to use the HTMLFeatures track type in order to get those right-click menu items (and Draggable behavior) instead of CanvasFeatures. Sorry about the confusion!
Maybe we'll get to add CanvasFeatures support in a later release

-Colin


On Fri, Apr 4, 2014 at 12:49 PM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

We just updated to the latest version of WebApollo, and I still don't see a "Create new annotation" option when I right click on the evidence in the static tracks (see attached screen shot) in order to make a non-coding RNA model. Am I misunderstanding what you meant?

Thanks,
Kyle


On Fri, Mar 21, 2014 at 4:04 PM, Ed Lee <[hidden email]> wrote:
Hi Kyle,

Are you running the latest version of WebApollo?  The ability to create annotations other than coding transcripts was added in the latest release (2013-11-22).

Cheers,
Ed


On Fri, Mar 21, 2014 at 9:54 AM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

When I right click a static track, the option to "Create new annotation" does not come up (see attached screen shot example). Am I misinterpreting what you mean?

Thanks,
Kyle


On Thu, Mar 20, 2014 at 4:11 PM, Ed Lee <[hidden email]> wrote:
Hi Kyle,

The easiest (and currently only =) ) way to annotate ncRNAs (or any non-protein coding transcript) is to select the evidence from the static tracks, right click, select "Create new annotation", and then select the appropriate type.

Cheers,
Ed


On Thu, Mar 20, 2014 at 11:49 AM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

Forgive me if this is a naive question, but what is the easiest way to annotate a non-coding RNA (i.e. rRNA/tRNA) in WebApollo? I have looked at the notes in the manual and am still having a lot of trouble with this.

Thanks,
Kyle

IGS
MMI
UMB







Screen Shot 2014-04-04 at 3.47.33 PM.png (75K) Download Attachment
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Re: Annotating ncRNAs

Ed Lee
Hi Kyle,

It seems like you're running the current WebApollo on an older data directory.  You'll need to update your data directory by running (in your JBrowse directory):

$ bin/add-webapollo-plugin.pl -i data/trackList.json

Check out the documentation for more info:


Hope this helps.

Cheers,
Ed


On Fri, Apr 4, 2014 at 12:51 PM, Kyle Tretina <[hidden email]> wrote:
Hi Colin,

The HTMLFeatures track was loaded with this command:
# ./bin/flatfile-to-json.pl --gff data/B_microti_4_chrom_plus_mito.tRNAscan-SE.gff3 --trackLabel "tRNAscan preds" --trackType HTMLFeatures

I could then see the "Create new annotation" option, but when I added the tRNA, I got the attached error message. Any ideas on what we need to change?

Thanks,
Kyle



On Fri, Apr 4, 2014 at 1:59 PM, Colin <[hidden email]> wrote:
Hi Kyle,
I think the issue is that you have to use the HTMLFeatures track type in order to get those right-click menu items (and Draggable behavior) instead of CanvasFeatures. Sorry about the confusion!
Maybe we'll get to add CanvasFeatures support in a later release

-Colin


On Fri, Apr 4, 2014 at 12:49 PM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

We just updated to the latest version of WebApollo, and I still don't see a "Create new annotation" option when I right click on the evidence in the static tracks (see attached screen shot) in order to make a non-coding RNA model. Am I misunderstanding what you meant?

Thanks,
Kyle


On Fri, Mar 21, 2014 at 4:04 PM, Ed Lee <[hidden email]> wrote:
Hi Kyle,

Are you running the latest version of WebApollo?  The ability to create annotations other than coding transcripts was added in the latest release (2013-11-22).

Cheers,
Ed


On Fri, Mar 21, 2014 at 9:54 AM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

When I right click a static track, the option to "Create new annotation" does not come up (see attached screen shot example). Am I misinterpreting what you mean?

Thanks,
Kyle


On Thu, Mar 20, 2014 at 4:11 PM, Ed Lee <[hidden email]> wrote:
Hi Kyle,

The easiest (and currently only =) ) way to annotate ncRNAs (or any non-protein coding transcript) is to select the evidence from the static tracks, right click, select "Create new annotation", and then select the appropriate type.

Cheers,
Ed


On Thu, Mar 20, 2014 at 11:49 AM, Kyle Tretina <[hidden email]> wrote:
Hi Ed,

Forgive me if this is a naive question, but what is the easiest way to annotate a non-coding RNA (i.e. rRNA/tRNA) in WebApollo? I have looked at the notes in the manual and am still having a lot of trouble with this.

Thanks,
Kyle

IGS
MMI
UMB