Showing a GC content track in Apollo

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Showing a GC content track in Apollo

abhijit.synl@gmail.com
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.synl@gmail.com
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.







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Re: Showing a GC content track in Apollo

abhijit.synl@gmail.com
In reply to this post by Eric Rasche-3
Hi Eric Rasche,

Sometime back I had asked about a plugin in Apollo that would enable me to observe GC-Content. To that you had directed me to the gccontent plugin that is used by you'll. Below is your message from the Apollo mailing list.
=======================================================================================
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
=======================================================================================

I have made changes to the apollo-config.groovy file, and installed the plugin under the JBrowse plugin folder in Apollo. However, I am not able to see the tracks. What do I need to do post this change. I am working on a linux system. I have used the following commands so far 

1) bin/prepare-refseqs.pl --fasta /path/to/foo.fasta --out /opt/annotation/data/
2) bin/flatfile-to-json.pl --gff path/to/foo.gff3 --arrowheadClass trellis-arrowhead --subfeatureClasses '{"CDS":"brightgreen-80pct", "five_prime_UTR":"darkblue-60pct", "three_prime_UTR":"darkblue-60pct", "exon":"container-100pct"}' --className container-16px --type mRNA --trackLabel GSAP-Models --out /opt/annotation/data/

To enable the GCContent is there a script that needs to be run? I am confused what to do here. Please guide me. 

Thank you,
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.







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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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Re: Showing a GC content track in Apollo

Deepak Unni
Hi Abhijit,

After adding the GCContent plugin to apollo-config.groovy and installing the plugin in the JBrowse plugin folder, you still need to configure the GC content track in trackList.json corresponding to the data directory for your organism.

This can be achieved by adding the following to your trackList.json,
      {
        "storeClass" : "JBrowse/Store/SeqFeature/SequenceChunks",
        "type": "GCContent/View/Track/GCContentXY",
        "label" : "GCContentXY",
        "label" : "GC Content",
        "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
        "bicolor_pivot": 0.5
      },


You will also have to rename the track with label "DNA" to "refseqs" for this to work. 
These configurations (and more) are available here: https://github.com/elsiklab/gccontent

After adding the suggested changes you should be able to see a new track, called 'GC Content', show up in JBrowse and Apollo. 


Hope this helps.

Cheers,

Deepak



On Fri, Aug 18, 2017 at 5:46 AM, Abhijit Sanyal <[hidden email]> wrote:
Hi Eric Rasche,

Sometime back I had asked about a plugin in Apollo that would enable me to observe GC-Content. To that you had directed me to the gccontent plugin that is used by you'll. Below is your message from the Apollo mailing list.
=======================================================================================
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
=======================================================================================

I have made changes to the apollo-config.groovy file, and installed the plugin under the JBrowse plugin folder in Apollo. However, I am not able to see the tracks. What do I need to do post this change. I am working on a linux system. I have used the following commands so far 

1) bin/prepare-refseqs.pl --fasta /path/to/foo.fasta --out /opt/annotation/data/
2) bin/flatfile-to-json.pl --gff path/to/foo.gff3 --arrowheadClass trellis-arrowhead --subfeatureClasses '{"CDS":"brightgreen-80pct", "five_prime_UTR":"darkblue-60pct", "three_prime_UTR":"darkblue-60pct", "exon":"container-100pct"}' --className container-16px --type mRNA --trackLabel GSAP-Models --out /opt/annotation/data/

To enable the GCContent is there a script that needs to be run? I am confused what to do here. Please guide me. 

Thank you,
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.







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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.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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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Re: Showing a GC content track in Apollo

abhijit.synl@gmail.com
Hi Deepak,

Right at the beginning of the "trackList.json" file there is the following json code block

   "tracks" : [
      {
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "chunkSize" : 20000,
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "label" : "DNA",
         "type" : "SequenceTrack",
         "category" : "Reference sequence",
         "seqType" : "dna",
         "key" : "Reference sequence"
      },

You are asking me to change "label" : "DNA", to "label" : "refseq" in the beginning of the file. Is that correct?

Second Question:
Do I have to do this after every run of prepare_refseqs.pl? Is there a method to automate these config changes?

Please let me know. I have copied a few other folks who are helping me set this up.

Thanks for your help.
Abhijit

On Fri, Aug 18, 2017 at 11:11 PM, Deepak Unni <[hidden email]> wrote:
Hi Abhijit,

After adding the GCContent plugin to apollo-config.groovy and installing the plugin in the JBrowse plugin folder, you still need to configure the GC content track in trackList.json corresponding to the data directory for your organism.

This can be achieved by adding the following to your trackList.json,
      {
        "storeClass" : "JBrowse/Store/SeqFeature/SequenceChunks",
        "type": "GCContent/View/Track/GCContentXY",
        "label" : "GCContentXY",
        "label" : "GC Content",
        "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
        "bicolor_pivot": 0.5
      },


You will also have to rename the track with label "DNA" to "refseqs" for this to work. 
These configurations (and more) are available here: https://github.com/elsiklab/gccontent

After adding the suggested changes you should be able to see a new track, called 'GC Content', show up in JBrowse and Apollo. 


Hope this helps.

Cheers,

Deepak



On Fri, Aug 18, 2017 at 5:46 AM, Abhijit Sanyal <[hidden email]> wrote:
Hi Eric Rasche,

Sometime back I had asked about a plugin in Apollo that would enable me to observe GC-Content. To that you had directed me to the gccontent plugin that is used by you'll. Below is your message from the Apollo mailing list.
=======================================================================================
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
=======================================================================================

I have made changes to the apollo-config.groovy file, and installed the plugin under the JBrowse plugin folder in Apollo. However, I am not able to see the tracks. What do I need to do post this change. I am working on a linux system. I have used the following commands so far 

1) bin/prepare-refseqs.pl --fasta /path/to/foo.fasta --out /opt/annotation/data/
2) bin/flatfile-to-json.pl --gff path/to/foo.gff3 --arrowheadClass trellis-arrowhead --subfeatureClasses '{"CDS":"brightgreen-80pct", "five_prime_UTR":"darkblue-60pct", "three_prime_UTR":"darkblue-60pct", "exon":"container-100pct"}' --className container-16px --type mRNA --trackLabel GSAP-Models --out /opt/annotation/data/

To enable the GCContent is there a script that needs to be run? I am confused what to do here. Please guide me. 

Thank you,
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.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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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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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Re: Showing a GC content track in Apollo

Deepak Unni
Hi Abhijit,

1. Yes, that is correct. But change it to 'refseqs', and not 'refseq', such that it looks like this:

   "tracks" : [
      {
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "chunkSize" : 20000,
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "label" : "refseqs",
         "type" : "SequenceTrack",
         "category" : "Reference sequence",
         "seqType" : "dna",
         "key" : "Reference sequence"
      },


2. Once the plugin is added to JBrowse (a one time configuration), you will have to add the GCContent track to trackList.json and change the DNA track label to 'refseqs' for every organism. Thus, each time you parse a fasta file via prepare_refseqs.pl you will have to modify the resulting trackList.json.

There is no automation scripts since this configuration is pretty straightforward. You could probably write a script that runs prepare_refseqs.pl and then make the modifications to trackList.json such that it can be abstracted as a single step.


Hope this helps.

Cheers,

Deepak

On Wed, Aug 23, 2017 at 1:34 AM, Abhijit Sanyal <[hidden email]> wrote:
Hi Deepak,

Right at the beginning of the "trackList.json" file there is the following json code block

   "tracks" : [
      {
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "chunkSize" : 20000,
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "label" : "DNA",
         "type" : "SequenceTrack",
         "category" : "Reference sequence",
         "seqType" : "dna",
         "key" : "Reference sequence"
      },

You are asking me to change "label" : "DNA", to "label" : "refseq" in the beginning of the file. Is that correct?

Second Question:
Do I have to do this after every run of prepare_refseqs.pl? Is there a method to automate these config changes?

Please let me know. I have copied a few other folks who are helping me set this up.

Thanks for your help.
Abhijit

On Fri, Aug 18, 2017 at 11:11 PM, Deepak Unni <[hidden email]> wrote:
Hi Abhijit,

After adding the GCContent plugin to apollo-config.groovy and installing the plugin in the JBrowse plugin folder, you still need to configure the GC content track in trackList.json corresponding to the data directory for your organism.

This can be achieved by adding the following to your trackList.json,
      {
        "storeClass" : "JBrowse/Store/SeqFeature/SequenceChunks",
        "type": "GCContent/View/Track/GCContentXY",
        "label" : "GCContentXY",
        "label" : "GC Content",
        "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
        "bicolor_pivot": 0.5
      },


You will also have to rename the track with label "DNA" to "refseqs" for this to work. 
These configurations (and more) are available here: https://github.com/elsiklab/gccontent

After adding the suggested changes you should be able to see a new track, called 'GC Content', show up in JBrowse and Apollo. 


Hope this helps.

Cheers,

Deepak



On Fri, Aug 18, 2017 at 5:46 AM, Abhijit Sanyal <[hidden email]> wrote:
Hi Eric Rasche,

Sometime back I had asked about a plugin in Apollo that would enable me to observe GC-Content. To that you had directed me to the gccontent plugin that is used by you'll. Below is your message from the Apollo mailing list.
=======================================================================================
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
=======================================================================================

I have made changes to the apollo-config.groovy file, and installed the plugin under the JBrowse plugin folder in Apollo. However, I am not able to see the tracks. What do I need to do post this change. I am working on a linux system. I have used the following commands so far 

1) bin/prepare-refseqs.pl --fasta /path/to/foo.fasta --out /opt/annotation/data/
2) bin/flatfile-to-json.pl --gff path/to/foo.gff3 --arrowheadClass trellis-arrowhead --subfeatureClasses '{"CDS":"brightgreen-80pct", "five_prime_UTR":"darkblue-60pct", "three_prime_UTR":"darkblue-60pct", "exon":"container-100pct"}' --className container-16px --type mRNA --trackLabel GSAP-Models --out /opt/annotation/data/

To enable the GCContent is there a script that needs to be run? I am confused what to do here. Please guide me. 

Thank you,
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.







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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.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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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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Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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.