add a new exon based on Bigwig file

classic Classic list List threaded Threaded
7 messages Options
Reply | Threaded
Open this post in threaded view
|

add a new exon based on Bigwig file

Quanwei Zhang
Hello:

It seems the first exon is missing in our predicted gene model. We observed this through the RNA-seq alignment track. How can I add the missing exon into "user-created Annotation" gene model. Please see the attached file for my case.

In the manual it says "select and drag the putative new exon from a track in the ‘Evidence’ panel". But now the evidence is from Bigwig track, which is not an exon. I can not select and drag it.

Do you have any suggestion?

Thanks




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.


addNeeExon.pdf (373K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: add a new exon based on Bigwig file

nathandunn


Its unfortunate you don’t have any further evidence to back up your BigWig as that would be the easiest solution.  Do you not have a GFF3 file that corresponds to it?   This would be the preferred method for a number of reasons.

The other way to do this, which I would discourage in lieu of creating another track would be to drag up another exon by itself from the evidence  (which will create a separate transcript), move it into the correct upstream via multiple dragging and then select both transcripts and finally select “merge transcripts”.  Ugly, but it will work.

Nathan


> On Jan 18, 2019, at 11:30 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Hello:
>
> It seems the first exon is missing in our predicted gene model. We observed this through the RNA-seq alignment track. How can I add the missing exon into "user-created Annotation" gene model. Please see the attached file for my case.
>
> In the manual it says "select and drag the putative new exon from a track in the ‘Evidence’ panel". But now the evidence is from Bigwig track, which is not an exon. I can not select and drag it.
>
> Do you have any suggestion?
>
> Thanks
> <addNeeExon.pdf>
>
>
> 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.

Reply | Threaded
Open this post in threaded view
|

Re: add a new exon based on Bigwig file

Quanwei Zhang
Yes. I have the GFF3. So I can change the GFF3 file directly and then upload it.

Thanks

Best
Quanwei

Nathan Dunn <[hidden email]> 于2019年1月18日周五 下午2:53写道:


Its unfortunate you don’t have any further evidence to back up your BigWig as that would be the easiest solution.  Do you not have a GFF3 file that corresponds to it?   This would be the preferred method for a number of reasons.

The other way to do this, which I would discourage in lieu of creating another track would be to drag up another exon by itself from the evidence  (which will create a separate transcript), move it into the correct upstream via multiple dragging and then select both transcripts and finally select “merge transcripts”.  Ugly, but it will work.

Nathan


> On Jan 18, 2019, at 11:30 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Hello:
>
> It seems the first exon is missing in our predicted gene model. We observed this through the RNA-seq alignment track. How can I add the missing exon into "user-created Annotation" gene model. Please see the attached file for my case.
>
> In the manual it says "select and drag the putative new exon from a track in the ‘Evidence’ panel". But now the evidence is from Bigwig track, which is not an exon. I can not select and drag it.
>
> Do you have any suggestion?
>
> Thanks
> <addNeeExon.pdf>
>
>
> 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/
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.

Reply | Threaded
Open this post in threaded view
|

Re: add a new exon based on Bigwig file

nathandunn
Well, you could do that as well, but that’s not what I was suggesting (and it’s not necessary).

I’m not sure what your bigwig track is indicating or why your gene predictor didn’t think there was an exon there. 

Do you have reads in that area or other predictions that provide evidence? 

Nathan

On Jan 18, 2019, at 1:50 PM, Quanwei Zhang <[hidden email]> wrote:

Yes. I have the GFF3. So I can change the GFF3 file directly and then upload it.

Thanks

Best
Quanwei

Nathan Dunn <[hidden email]> 于2019年1月18日周五 下午2:53写道:


Its unfortunate you don’t have any further evidence to back up your BigWig as that would be the easiest solution.  Do you not have a GFF3 file that corresponds to it?   This would be the preferred method for a number of reasons.

The other way to do this, which I would discourage in lieu of creating another track would be to drag up another exon by itself from the evidence  (which will create a separate transcript), move it into the correct upstream via multiple dragging and then select both transcripts and finally select “merge transcripts”.  Ugly, but it will work.

Nathan


> On Jan 18, 2019, at 11:30 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Hello:
>
> It seems the first exon is missing in our predicted gene model. We observed this through the RNA-seq alignment track. How can I add the missing exon into "user-created Annotation" gene model. Please see the attached file for my case.
>
> In the manual it says "select and drag the putative new exon from a track in the ‘Evidence’ panel". But now the evidence is from Bigwig track, which is not an exon. I can not select and drag it.
>
> Do you have any suggestion?
>
> Thanks
> <addNeeExon.pdf>
>
>
> 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/
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.

Reply | Threaded
Open this post in threaded view
|

Re: add a new exon based on Bigwig file

Quanwei Zhang
I don't know why MAKER did not predict that exon, based on the RNA-seq alignment and also protein sequence alignment with orthologs, we found the first exon is missing.
Thanks

Lbl <[hidden email]> 于2019年1月18日周五 下午5:43写道:
Well, you could do that as well, but that’s not what I was suggesting (and it’s not necessary).

I’m not sure what your bigwig track is indicating or why your gene predictor didn’t think there was an exon there. 

Do you have reads in that area or other predictions that provide evidence? 

Nathan

On Jan 18, 2019, at 1:50 PM, Quanwei Zhang <[hidden email]> wrote:

Yes. I have the GFF3. So I can change the GFF3 file directly and then upload it.

Thanks

Best
Quanwei

Nathan Dunn <[hidden email]> 于2019年1月18日周五 下午2:53写道:


Its unfortunate you don’t have any further evidence to back up your BigWig as that would be the easiest solution.  Do you not have a GFF3 file that corresponds to it?   This would be the preferred method for a number of reasons.

The other way to do this, which I would discourage in lieu of creating another track would be to drag up another exon by itself from the evidence  (which will create a separate transcript), move it into the correct upstream via multiple dragging and then select both transcripts and finally select “merge transcripts”.  Ugly, but it will work.

Nathan


> On Jan 18, 2019, at 11:30 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Hello:
>
> It seems the first exon is missing in our predicted gene model. We observed this through the RNA-seq alignment track. How can I add the missing exon into "user-created Annotation" gene model. Please see the attached file for my case.
>
> In the manual it says "select and drag the putative new exon from a track in the ‘Evidence’ panel". But now the evidence is from Bigwig track, which is not an exon. I can not select and drag it.
>
> Do you have any suggestion?
>
> Thanks
> <addNeeExon.pdf>
>
>
> 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/
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/
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.

Reply | Threaded
Open this post in threaded view
|

Re: add a new exon based on Bigwig file

nathandunn

I couldn’t tell you.   I would agree that it looks like it is missing.   Might be worth posting to the MAKER forum to see why, but if you are confident, that my suggestion about adding the extra exon is okay, as well. 

Nathan

On Jan 19, 2019, at 5:13 AM, Quanwei Zhang <[hidden email]> wrote:

I don't know why MAKER did not predict that exon, based on the RNA-seq alignment and also protein sequence alignment with orthologs, we found the first exon is missing.
Thanks

Lbl <[hidden email]> 于2019年1月18日周五 下午5:43写道:
Well, you could do that as well, but that’s not what I was suggesting (and it’s not necessary).

I’m not sure what your bigwig track is indicating or why your gene predictor didn’t think there was an exon there. 

Do you have reads in that area or other predictions that provide evidence? 

Nathan

On Jan 18, 2019, at 1:50 PM, Quanwei Zhang <[hidden email]> wrote:

Yes. I have the GFF3. So I can change the GFF3 file directly and then upload it.

Thanks

Best
Quanwei

Nathan Dunn <[hidden email]> 于2019年1月18日周五 下午2:53写道:


Its unfortunate you don’t have any further evidence to back up your BigWig as that would be the easiest solution.  Do you not have a GFF3 file that corresponds to it?   This would be the preferred method for a number of reasons.

The other way to do this, which I would discourage in lieu of creating another track would be to drag up another exon by itself from the evidence  (which will create a separate transcript), move it into the correct upstream via multiple dragging and then select both transcripts and finally select “merge transcripts”.  Ugly, but it will work.

Nathan


> On Jan 18, 2019, at 11:30 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Hello:
>
> It seems the first exon is missing in our predicted gene model. We observed this through the RNA-seq alignment track. How can I add the missing exon into "user-created Annotation" gene model. Please see the attached file for my case.
>
> In the manual it says "select and drag the putative new exon from a track in the ‘Evidence’ panel". But now the evidence is from Bigwig track, which is not an exon. I can not select and drag it.
>
> Do you have any suggestion?
>
> Thanks
> <addNeeExon.pdf>
>
>
> 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/
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/
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.

Reply | Threaded
Open this post in threaded view
|

Re: add a new exon based on Bigwig file

Quanwei Zhang
Thank you!

Nathan Dunn <[hidden email]> 于2019年1月19日周六 下午12:40写道:

I couldn’t tell you.   I would agree that it looks like it is missing.   Might be worth posting to the MAKER forum to see why, but if you are confident, that my suggestion about adding the extra exon is okay, as well. 

Nathan

On Jan 19, 2019, at 5:13 AM, Quanwei Zhang <[hidden email]> wrote:

I don't know why MAKER did not predict that exon, based on the RNA-seq alignment and also protein sequence alignment with orthologs, we found the first exon is missing.
Thanks

Lbl <[hidden email]> 于2019年1月18日周五 下午5:43写道:
Well, you could do that as well, but that’s not what I was suggesting (and it’s not necessary).

I’m not sure what your bigwig track is indicating or why your gene predictor didn’t think there was an exon there. 

Do you have reads in that area or other predictions that provide evidence? 

Nathan

On Jan 18, 2019, at 1:50 PM, Quanwei Zhang <[hidden email]> wrote:

Yes. I have the GFF3. So I can change the GFF3 file directly and then upload it.

Thanks

Best
Quanwei

Nathan Dunn <[hidden email]> 于2019年1月18日周五 下午2:53写道:


Its unfortunate you don’t have any further evidence to back up your BigWig as that would be the easiest solution.  Do you not have a GFF3 file that corresponds to it?   This would be the preferred method for a number of reasons.

The other way to do this, which I would discourage in lieu of creating another track would be to drag up another exon by itself from the evidence  (which will create a separate transcript), move it into the correct upstream via multiple dragging and then select both transcripts and finally select “merge transcripts”.  Ugly, but it will work.

Nathan


> On Jan 18, 2019, at 11:30 AM, Quanwei Zhang <[hidden email]> wrote:
>
> Hello:
>
> It seems the first exon is missing in our predicted gene model. We observed this through the RNA-seq alignment track. How can I add the missing exon into "user-created Annotation" gene model. Please see the attached file for my case.
>
> In the manual it says "select and drag the putative new exon from a track in the ‘Evidence’ panel". But now the evidence is from Bigwig track, which is not an exon. I can not select and drag it.
>
> Do you have any suggestion?
>
> Thanks
> <addNeeExon.pdf>
>
>
> 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/
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/
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/
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.