Showing a GC content track in Apollo

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Showing a GC content track in Apollo

Abhijit Sanyal
Hello,

A few questions on Apollo 2.0.4

1) How do I display a GC-content track in Apollo? I did not find a suitable script in the bin directory.

2) What is the process for displaying ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, transposable elements, TSS? Any step-by-step process available for reference?

3) Can Apollo handle large volumes of read data? During annotation I am sometimes concerned about the quality of the target sequence. Can Apollo help me make that call by visualizing the quality at a particular site/s of the target sequence

Best Regards
Abhijit




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Re: Showing a GC content track in Apollo

Eric Rasche-3
It works well for our case. Calculates the gc content/skew on the fly. Easy to add once to our apollo instance, and then is available in every organism loaded within our Apollo.

E.g. in our modified apollo-config.groovy:
https://github.com/erasche/docker-apollo/blob/cpt/apollo-config.groovy#L131



2017-06-28 7:13 GMT+00:00 Abhijit Sanyal <[hidden email]>:
Hello,

A few questions on Apollo 2.0.4

1) How do I display a GC-content track in Apollo? I did not find a suitable script in the bin directory.

2) What is the process for displaying ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, transposable elements, TSS? Any step-by-step process available for reference?

3) Can Apollo handle large volumes of read data? During annotation I am sometimes concerned about the quality of the target sequence. Can Apollo help me make that call by visualizing the quality at a particular site/s of the target sequence

Best Regards
Abhijit




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.





--
Eric Rasche
Software Application Developer II

Center for Phage Technology
Texas A&M University
College Station, TX 77843




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Re: Showing a GC content track in Apollo

Abhijit Sanyal
Hi Eric,

Thank you for the fast response. I am in the process of implementing the same. I'll write back if I have trouble. Thank for sharing your config file setup with me.

-Abhijit

On Wed, Jun 28, 2017 at 12:49 PM, Eric Rasche <[hidden email]> wrote:
It works well for our case. Calculates the gc content/skew on the fly. Easy to add once to our apollo instance, and then is available in every organism loaded within our Apollo.

E.g. in our modified apollo-config.groovy:
https://github.com/erasche/docker-apollo/blob/cpt/apollo-config.groovy#L131



2017-06-28 7:13 GMT+00:00 Abhijit Sanyal <[hidden email]>:
Hello,

A few questions on Apollo 2.0.4

1) How do I display a GC-content track in Apollo? I did not find a suitable script in the bin directory.

2) What is the process for displaying ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, transposable elements, TSS? Any step-by-step process available for reference?

3) Can Apollo handle large volumes of read data? During annotation I am sometimes concerned about the quality of the target sequence. Can Apollo help me make that call by visualizing the quality at a particular site/s of the target sequence

Best Regards
Abhijit




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.





--
Eric Rasche
Software Application Developer II

Center for Phage Technology
Texas A&M University
College Station, TX 77843




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.

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