Name: The annotation table
Topic: for students side > Additional Analyses
Outline:
Generating the genome annotation table
a. Retrieve Data from Apollo
b. Run the Annotation Table tool: Annotation Table from gff3 formatted datasets (Galaxy Version 4.0).
c. Use retrieved data as input. Select tabular table as the report format output.
d. Download the annotation table to your local machine by clicking on the save/download icon in the expanded dataset view within the history.
e. Open the genome annotation table in a spreadsheet.
Uses for the genome annotation table
a. Viewing all names and notes associated with features in an Apollo record
i. Remember, this is a snapshot in time and does not update when things are changed in Apollo. The annotation table can be generated again at any time. Using the annotation table as a temporary holding place for names and notes is fine as viewing these next to each other can be convenient. In a way it also doubles the amount of work in assigning functional predictions since the values have to manually entered into Apollo.
ii. Could help you organize your thoughts, impressions, and notes relevant to consider when trying to decide on a final name. They are all right next to each other if opened in an excel-type spreadsheet.
iii. Reduces all the clicking required to simply view notes for any feature in Apollo.
b. A future goal is to be able to convert the changes made in the annotation table back into the gff3 file so that Apollo can also be updated.
i. Doing it this way would allow mass application of needed changes for misspelling, capitalization problems, or other formatting issues with the name and notes text.
jrr-cpt
commented
4 years ago
@ToniNittolo
Name: The annotation table Topic: for students side > Additional Analyses Outline:
Generating the genome annotation table a. Retrieve Data from Apollo b. Run the Annotation Table tool: Annotation Table from gff3 formatted datasets (Galaxy Version 4.0). c. Use retrieved data as input. Select tabular table as the report format output. d. Download the annotation table to your local machine by clicking on the save/download icon in the expanded dataset view within the history. e. Open the genome annotation table in a spreadsheet.
Uses for the genome annotation table a. Viewing all names and notes associated with features in an Apollo record i. Remember, this is a snapshot in time and does not update when things are changed in Apollo. The annotation table can be generated again at any time. Using the annotation table as a temporary holding place for names and notes is fine as viewing these next to each other can be convenient. In a way it also doubles the amount of work in assigning functional predictions since the values have to manually entered into Apollo. ii. Could help you organize your thoughts, impressions, and notes relevant to consider when trying to decide on a final name. They are all right next to each other if opened in an excel-type spreadsheet. iii. Reduces all the clicking required to simply view notes for any feature in Apollo. b. A future goal is to be able to convert the changes made in the annotation table back into the gff3 file so that Apollo can also be updated. i. Doing it this way would allow mass application of needed changes for misspelling, capitalization problems, or other formatting issues with the name and notes text.