Difference between revisions of "FlyBase:GBrowse Help"
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| − | == | + | ==Navigating around the Genome== |
| − | + | ===Choosing a genome=== | |
| − | + | The genome is set to D. melanogaster by default, but other Drosophila genomes are available using the Data Source box in the search panel. | |
| − | + | Available genomes are: | |
| − | + | * D. pseudoobscura | |
| − | + | * D. ananaassae | |
| − | + | * D. erecta | |
| − | + | * D. grimshawi | |
| − | + | * D. mojavensis | |
| − | + | * D. persimilis | |
| − | == | + | * D. sechelia |
| + | |||
| + | * D. simulans | ||
| + | |||
| + | * D. virilis | ||
| + | |||
| + | * D. wilistoni | ||
| + | |||
| + | * D. yakuba | ||
| + | |||
| + | ===Finding a specific region of the genome=== | ||
| + | |||
| + | To select a region of the chosen genome to view, enter its name in the text field labeled "Landmark or Region". This box will accept: | ||
| + | |||
| + | * '''FlyBase symbols''', eg cnn | ||
| + | |||
| + | * '''FlyBase IDs''' eg FBgn0000490 | ||
| + | |||
| + | * '''Sequence locations''' eg X:6000..8000, 2L:80,000..100,000 | ||
| + | |||
| + | To select a sub region of the region already displayed, click and drag in the coordinate scale in the detail panel. | ||
| + | |||
| + | To move to a different section of the chromosome, click on the chromosome scale in the Overview panel. The region of the chromosome that is currently displayed in the detail panel is indicated with two dotted lines. | ||
| + | |||
| + | ===Moving across the genome=== | ||
| + | |||
| + | Once a region of the genome is displayed there are two ways you can move across the genome from that location. | ||
| + | |||
| + | '''Using scroll buttons''' - Scroll defined distances left or right with the <<, <, > and >> buttons in the search panel. A pop up will indicate the distance that each button will scroll. | ||
| + | |||
| + | '''Dragging the detail panel''' - drag the detail panel left or right to move across the genome. | ||
| + | |||
| + | ==Customizing the display== | ||
| + | |||
| + | ===Zooming=== | ||
| + | |||
| + | Zoom in or out using the "Show XXX bp" menu in the search panel. The available options are: | ||
| + | |||
| + | * 100bp | ||
| + | * 200bp | ||
| + | * 1kbp | ||
| + | * 2kbp | ||
| + | * 5kbp | ||
| + | * 10kbp | ||
| + | * 20kbp | ||
| + | * 40kbp | ||
| + | * 70kbp | ||
| + | * 100kbp | ||
| + | * 200kbp | ||
| + | |||
| + | Press the - and + buttons either side of the menu to change the zoom level by 10%. | ||
| + | |||
| + | ===Centering=== | ||
| + | |||
| + | Click on the coordinate scale (at the top of the detail panel) to recenter the detail panel around the location you clicked. | ||
| + | |||
| + | ===Flipping the genome=== | ||
| + | |||
| + | To flip the browser display so that the minus strand points to the right, select the "flip" checkbox in the search panel. | ||
| + | |||
| + | ===Displaying restriction sites=== | ||
| + | |||
| + | Restriction sites can be displayed by choosing 'Annotate Restriction Sites" from the top right hand drop down box. Click 'Configure' to choose the restriction sites you would like to display. | ||
| + | |||
| + | ===Changing the order of the tracks=== | ||
| + | |||
| + | To change the order of the tracks in the display panel click on the track label and drag up or down. | ||
| + | |||
| + | ===Opening/closing panels=== | ||
| + | |||
| + | Click on the red add/minus sign at the top of each panel to open and close that panel. | ||
| + | |||
| + | ===Other display preferences=== | ||
| + | |||
| + | A number of other display preferences can be found in the Preferences tab including | ||
| + | |||
| + | * Showing/hiding the grid lines on the detail panel. These are displayed by default. | ||
| + | * Enabling/disabling caching of tracks. | ||
| + | * Show/hide tooltips. These are displayed by default. | ||
| + | * Changing the width of the image. The default image width is 800. Other options are 1024 and 2048. | ||
| + | ?? | ||
| + | |||
| + | ==Choosing tracks== | ||
| + | |||
| + | The default GBrowse view comprises a predetermined set of 10 tracks. For details of all of the tracks available see [[FlyBase:GBrowse_Tracks|here]] | ||
| + | |||
| + | ===Selecting existing tracks=== | ||
| + | |||
| + | To select tracks go to the 'Select Tracks' tab and choose the tracks you would like to display. | ||
| + | |||
| + | ===Adding custom racks=== | ||
| + | |||
| + | To add custom tracks go to the 'Custom Tracks' tab. | ||
| + | |||
| + | You have the option of adding tracks from text, from a URL or from a file. | ||
| + | |||
| + | For more information about how to add custom tracks see [http://{{SERVERNAME}}/.gb2/annotation_help.html here] | ||
| + | |||
| + | ==Customizing tracks== | ||
Favorites | Favorites | ||
| Line 37: | Line 135: | ||
==Other useful features== | ==Other useful features== | ||
| − | Saving as a picture | + | ===Saving as a picture=== |
| − | |||
| − | |||
| − | + | ===Ruler=== | |
| − | Download Decorated FASTA etc | + | ===Download Decorated FASTA etc=== |
| − | Links to report pages | + | ===Links to report pages=== |
| − | + | ===Accessing previous versions of the genome=== | |
Revision as of 12:11, 2 September 2015
Choosing a genome
The genome is set to D. melanogaster by default, but other Drosophila genomes are available using the Data Source box in the search panel.
Available genomes are:
- D. pseudoobscura
- D. ananaassae
- D. erecta
- D. grimshawi
- D. mojavensis
- D. persimilis
- D. sechelia
- D. simulans
- D. virilis
- D. wilistoni
- D. yakuba
Finding a specific region of the genome
To select a region of the chosen genome to view, enter its name in the text field labeled "Landmark or Region". This box will accept:
- FlyBase symbols, eg cnn
- FlyBase IDs eg FBgn0000490
- Sequence locations eg X:6000..8000, 2L:80,000..100,000
To select a sub region of the region already displayed, click and drag in the coordinate scale in the detail panel.
To move to a different section of the chromosome, click on the chromosome scale in the Overview panel. The region of the chromosome that is currently displayed in the detail panel is indicated with two dotted lines.
Moving across the genome
Once a region of the genome is displayed there are two ways you can move across the genome from that location.
Using scroll buttons - Scroll defined distances left or right with the <<, <, > and >> buttons in the search panel. A pop up will indicate the distance that each button will scroll.
Dragging the detail panel - drag the detail panel left or right to move across the genome.
Customizing the display
Zooming
Zoom in or out using the "Show XXX bp" menu in the search panel. The available options are:
- 100bp
- 200bp
- 1kbp
- 2kbp
- 5kbp
- 10kbp
- 20kbp
- 40kbp
- 70kbp
- 100kbp
- 200kbp
Press the - and + buttons either side of the menu to change the zoom level by 10%.
Centering
Click on the coordinate scale (at the top of the detail panel) to recenter the detail panel around the location you clicked.
Flipping the genome
To flip the browser display so that the minus strand points to the right, select the "flip" checkbox in the search panel.
Displaying restriction sites
Restriction sites can be displayed by choosing 'Annotate Restriction Sites" from the top right hand drop down box. Click 'Configure' to choose the restriction sites you would like to display.
Changing the order of the tracks
To change the order of the tracks in the display panel click on the track label and drag up or down.
Opening/closing panels
Click on the red add/minus sign at the top of each panel to open and close that panel.
Other display preferences
A number of other display preferences can be found in the Preferences tab including
- Showing/hiding the grid lines on the detail panel. These are displayed by default.
- Enabling/disabling caching of tracks.
- Show/hide tooltips. These are displayed by default.
- Changing the width of the image. The default image width is 800. Other options are 1024 and 2048.
??
Choosing tracks
The default GBrowse view comprises a predetermined set of 10 tracks. For details of all of the tracks available see here
Selecting existing tracks
To select tracks go to the 'Select Tracks' tab and choose the tracks you would like to display.
Adding custom racks
To add custom tracks go to the 'Custom Tracks' tab.
You have the option of adding tracks from text, from a URL or from a file.
For more information about how to add custom tracks see here
Customizing tracks
Favorites
Show or hide this track
Turn off this track
Share this track
Download this track
Configure this track
About track