Difference between revisions of "Documentation"
From GenPlay, Einstein Genome Analyzer
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== Loading a track == | == Loading a track == | ||
| − | To load a track in any row, right click on the handler of any empty track (the blue part | + | To load a track in any row, right click on the handler of any empty track (the blue part on the left of the track). This opens a menu including options to load the various types of tracks that exist in GenPlay. |
[[image:load_track.png|center|thumb|100px|Loading a Track]] | [[image:load_track.png|center|thumb|100px|Loading a Track]] | ||
| − | + | Examples of tracks that can be loaded in GenPlay are available for download from the GenPlay Library accessible from the GenPlay.net website. | |
=== Loading a variable window track === | === Loading a variable window track === | ||
[[image:load_vwt1.png|right|thumb|100px|File Chooser]] | [[image:load_vwt1.png|right|thumb|100px|File Chooser]] | ||
| − | Variable window tracks allow the visualization of windows of variable sizes with a score associated to | + | Variable window tracks allow the visualization of windows of variable sizes with a score associated to these windows. |
Select the “Load Variable Window Track” option. This opens up a file chooser dialog box. Load the file of your choice from the list of available fixed window files and click the open button. | Select the “Load Variable Window Track” option. This opens up a file chooser dialog box. Load the file of your choice from the list of available fixed window files and click the open button. | ||
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[[image:load_vwt2.png|left|thumb|100px|Chromosome Selection]] | [[image:load_vwt2.png|left|thumb|100px|Chromosome Selection]] | ||
==== Chromosome Selection ==== | ==== Chromosome Selection ==== | ||
| − | + | After selecting your file, a new window will appear and ask which chromosome to extract. By default all the chromosomes of the project are selected. If you want to change this selection, click on the "modify selection" button and uncheck the undesired chromosomes. Working on fewer chromosomes will save memory and loading time. | |
| − | '''Important Note:''' When specific chromosomes are selected, GenPlay works accurately | + | '''Important Note:''' When specific chromosomes are selected, GenPlay only works accurately if the files that are loaded are sorted by chromosomes. Unsorted files may load incompletely, leading to a loss of valuable information. |
==== Score Calculation ==== | ==== Score Calculation ==== | ||
| − | Once | + | Once the chromosome selection is done, a final window will pop-up and ask you to name the track. The default name is the loaded file name. If there are overlapping windows in your data file, you'll also be prompted to select a method for calculating the score of the windows. Overlapping windows will be split into smaller windows using a simple algorithm. |
[[image:load_vwt3.png|center|thumb|100px|Name and Score Calculation]] | [[image:load_vwt3.png|center|thumb|100px|Name and Score Calculation]] | ||
=== Loading Fixed Window Track === | === Loading Fixed Window Track === | ||
[[image:load_fwt1.png|left|thumb|100px|File Chooser]] | [[image:load_fwt1.png|left|thumb|100px|File Chooser]] | ||
| − | Fixed window tracks display bin lists are useful to represent the results of many types of experiments including CHIP-seq, RNA seq, TimEX-seq | + | Fixed window tracks display bin lists. They are useful to represent the results of many types of experiments including, but not limited to: CHIP-seq, RNA seq, and TimEX-seq. Files containing the results of alignments (SAM, bowtie, Eland) and files containing already created bin lists (bed, bgr, etc.) can be loaded using this option. In the case of alignment files, bin lists will be created on the fly as described below. Files containing the results of micro-array experiments can also be loaded as long as they are in one of the accepted formats. |
| − | + | By right clicking on an empty track handler, the contextual menu will pop up. Select the “Load Fixed Window Track” option. This opens up a file chooser dialog box as shown in the figure on the left. | |
| − | Load the track of your choice from the list of | + | |
| + | Load the track of your choice from the list of files and click the open button. Please refer to the [[#File formats|File formats]] section if you want to know what kind of file can be loaded as a fixed window track. | ||
==== Track Name ==== | ==== Track Name ==== | ||
[[image:load_fwt2.png|Right|thumb|200px|Fixed Window Track Options]] | [[image:load_fwt2.png|Right|thumb|200px|Fixed Window Track Options]] | ||
| − | + | The default track name will be the file name. The name of the track can also be change later after the track is loaded. | |
==== Window Size ==== | ==== Window Size ==== | ||
| − | This specifies the size in base pair (bp) | + | This specifies the size of the genomic windows (bins) in base pair (bp) for the track that will be created to summarize the results. |
==== Score Calculation ==== | ==== Score Calculation ==== | ||
| − | This option allows you to choose how the scores of the bins are calculated. You may choose between three options: average, maximum or sum. The algorithm of the score calculation is explained | + | This option allows you to choose how the scores of the bins are calculated. You may choose between three options: average, maximum or sum. The algorithm of the score calculation is explained below. |
==== Strand Selection ==== | ==== Strand Selection ==== | ||
| − | If your input file contains information regarding the | + | If your input file contains information regarding the strands, you'll be able to choose to load the data from either both or only one strand. You can also decide to shift the reads from both strands as shown in the figure below. |
==== Data precision ==== | ==== Data precision ==== | ||
Because GenPlay requires a lot of RAM memory, we provide the option of changing the precision at which the score for each bin is stored. | Because GenPlay requires a lot of RAM memory, we provide the option of changing the precision at which the score for each bin is stored. | ||
* Scores in 64 bit are stored in floating value double precision (which can represent extremely large numbers unlikely to be useful for genomic experiments). | * Scores in 64 bit are stored in floating value double precision (which can represent extremely large numbers unlikely to be useful for genomic experiments). | ||
| − | * Scores in 32 bit are stored in floating value single precision (which can also represent very large | + | * Scores in 32 bit are stored in floating value single precision (which can also represent very large numbers). |
| + | * Scores stored in 16 bits can range between - 3267.8 and +3267.7 (with one decimal place). | ||
* Scores stored in 8 bits can range between 0 and 255 (with no decimal). | * Scores stored in 8 bits can range between 0 and 255 (with no decimal). | ||
* Score in 1 bit can be equal to zero or 1 (useful to create masks for instance). | * Score in 1 bit can be equal to zero or 1 (useful to create masks for instance). | ||
| − | We recommend storing scores in 32 or 16 bits | + | |
| + | We recommend storing scores in 32 or 16 bits. | ||
==== Chromosome selection ==== | ==== Chromosome selection ==== | ||
| − | + | You can load either the whole genome or only specific chromosomes (which saves time and memory). | |
| − | '''Important Note:''' When specific chromosomes are selected, GenPlay works accurately | + | '''Important Note:''' When specific chromosomes are selected, GenPlay only works accurately if the files that are loaded are sorted by chromosomes. Unsorted files may load incompletely, leading to a loss of valuable information. |
| − | When the OK button is clicked, the track is loaded | + | When the OK button is clicked, the track is loaded in the location desired. |
=== Loading a gene track === | === Loading a gene track === | ||
[[image:gene_track.png|left|thumb||A Gene Track]] | [[image:gene_track.png|left|thumb||A Gene Track]] | ||
[[image:score_color.png|right|thumb|40px|Score Color]] | [[image:score_color.png|right|thumb|40px|Score Color]] | ||
| − | + | After right clicking on the empty track handler, select the “Load Gene Track” option. This opens up a file chooser dialog box that allows you to select the file that you want to load. Please refer to the [[#File formats|File formats]] section if you want to know what kind of file can be loaded as a gene track. | |
Once it's done, just wait until the loading is complete and the gene track will appear in the track you selected. | Once it's done, just wait until the loading is complete and the gene track will appear in the track you selected. | ||
| − | Note that the genes on the plus strand are in red and the genes on the minus strand are in blue. If the file contains expression values, the exons are color coded to represent the expression (red = high, blue = low as shown on the right). | + | |
| + | Note that the genes on the plus strand are in red and the genes on the minus strand are in blue. If the file contains expression values, the exons are color coded to represent the expression (red = high, blue = low, as shown on the right). | ||
=== Loading a sequence track === | === Loading a sequence track === | ||
| − | + | After right clicking on the empty track handler, select the “Load Sequence Track” option. This opens up a file chooser dialog box that allows you to select the file that you want to load. Please refer to the [[#File formats|File formats]] section if you want to know what kind of file can be loaded as a sequence track. | |
[[image:sequence_track.png|center|thumb|300px|A Sequence Track]] | [[image:sequence_track.png|center|thumb|300px|A Sequence Track]] | ||
| − | + | Sequence tracks show DNA sequences from .2bit files. | |
| + | |||
| + | The hg18, hg19, mm8 and mm9 sequence files can be downloaded from the [http://129.98.70.162/wiki/index.php/Library library] of GenPlay. | ||
=== Loading a SNP track === | === Loading a SNP track === | ||
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Select the “Load Repeat Track” option on the track contextual menu. This opens up a file chooser dialog box that allows you to select the file that you want to load. Please refer to the [[#File formats|File formats]] section if you want to know what kind of file can be loaded as a repeat track. | Select the “Load Repeat Track” option on the track contextual menu. This opens up a file chooser dialog box that allows you to select the file that you want to load. Please refer to the [[#File formats|File formats]] section if you want to know what kind of file can be loaded as a repeat track. | ||
| − | This track type | + | This track type displays repeats organized by family or class. |
=== Loading data from a DAS server === | === Loading data from a DAS server === | ||
| − | The distributed annotation system (DAS) is a client-server system in which a client can retrieve data from one or multiple | + | The distributed annotation system (DAS) is a client-server system in which a client can retrieve data from one or multiple servers. GenPlay can connect to any server that follows the DAS/1 protocol as specified by [http://www.biodas.org/wiki/DAS/1 BioDAS] |
[[image:DAS_dialog.png|left|thumb||DAS Dialog]] | [[image:DAS_dialog.png|left|thumb||DAS Dialog]] | ||
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Select the server from which you want to retrieve the data in the "Server" box. | Select the server from which you want to retrieve the data in the "Server" box. | ||
| − | Then | + | Then select the "Data Source". Most of the time, the Data Source corresponds to the reference genome that you want to work on. |
Once that's done you need to select the data that you want to retrieve in the "Data Type" box. | Once that's done you need to select the data that you want to retrieve in the "Data Type" box. | ||
| − | GenPlay can either generate a gene track or a variable window track from the | + | GenPlay can either generate a gene track or a variable window track from the retrieved data. You can select what type of output track you want in the "Generate" option. |
Finally, you can also choose to download data on only a part of the genome. This can be useful because retrieving data from a DAS server can be time consuming. | Finally, you can also choose to download data on only a part of the genome. This can be useful because retrieving data from a DAS server can be time consuming. | ||
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The order of the tracks in the right list will determine the order in which the tracks are printed. The track on top of the list will be printed on top the other tracks. You can change the order of the tracks by clicking on the name of a track in the right list and using the up and down arrow in the middle of the dialog. | The order of the tracks in the right list will determine the order in which the tracks are printed. The track on top of the list will be printed on top the other tracks. You can change the order of the tracks by clicking on the name of a track in the right list and using the up and down arrow in the middle of the dialog. | ||
| − | '''Note:''' in order to change the appearance of a the multi | + | '''Note:''' in order to change the appearance of a the multi curve track, you need to change the appearance of the tracks that appear in the multi curves track. |
=== Loading stripes === | === Loading stripes === | ||
Revision as of 00:10, 2 December 2010
Contents
- 1 Starting GenPlay
- 2 GUI Overview
- 3 Browsing the genome
- 4 Loading a track
- 5 Main Menu
- 6 Changing the configuration of GenPlay
- 7 File formats
- 8 Manipulating tracks
- 9 Using the operations
Starting GenPlay
GenPlay is freely available at http://www.genplay.net/wiki/index.php/Web_Start To start the software, click the button corresponding to the amount of memory that you wish to allocate to the Java virtual machine.
The amount of memory determines how many tracks you will be able to load simultaneously. The programming philosophy behind GenPlay is to provide extremely fast performances once the data is loaded. To achieve that goal the entire genome need to be loaded in memory for multiple tracks at the same time. This results in high quality performance, but requires a lot of memory. The amount of memory needed per track depends on the genome, the track type, the window size, the data precision etc.
You should generally choose as much memory as you can afford on your system (generally about 70% of the total RAM memory that exists on your system). For mammalian genomes we recommend allocating at least 4 GB of RAM although you should be able to load a couple of genome-wide tracks with 1GB or 1.5GB of RAM. Selecting analysis of only one chromosome at a time will drastically reduce the memory requirement and should allow you to load many tracks at very high resolutions. Tracks loaded in GenPlay can also be compressed as explained later in this documentation.
The amount of RAM memory available to GenPlay is displayed in the lower right corner of the screen.
GUI Overview
GenPlay main window is divided in 4 main parts:
- Ruler
- Track List
- Control Panel
- Status Bar
Ruler
The ruler shows the coordinates of the current displayed position.
General Option Button
The button on the left of the ruler opens the pop-up menu with all the general options.
Absolute Positions
The numbers written in red on top of the ruler are the absolute position on the selected chromosome or scaffold.
The number on the left is the position of the first displayed base. This value can be negative.
The number in the middle is the position of the red line. This value can go from 0 to the length of the current chromosome or scaffold as specified in the chromosome configuration file.
The value on the right is the last displayed position. This value range from 1 to 2*(chromosome length).
Relative Position
The numbers written in black on the second line represent the distance from the middle in base pair.
Track List
The track list is the cornerstone of the GUI. From here you can load tracks and execute operations.
The tracks are divided into two parts.
On the left, there is the track handler that becomes highlighted when the mouse is over it. By right clicking on the track handler, a contextual menu appears with all the operations that can be executed on the track.
On the right, the data can be visualized.
Control Panel
The control panel is divided into 4 parts:
- Position Bar: the position bar allows you to change the position of the current displayed windows
- Zoom Bar: use the zoom bar to modify the level of zoom
- Chromosome Box: set the selected chromosome with the chromosome box
- Position Text Field: the position text field follows the format of the UCSC Genome Browser position field so it is easy to copy and paste the position from one browser to the other
Status Bar
The status bar helps you to monitor the progress of the current operation as well as the memory usage. It is divided into 4 sub-components:
- Progress bar, shows the level of completion of the current operation
- Stop button, allows you to stop the current operation. If the button is not bright red the operation can't be stopped
- Operation description, displays a short text describing the current operation as well as the elapsed time from the beginning of the operation
- Memory bar, shows the amount of memory used and the amount of memory available. Make sure that you have enough memory before starting a new operation. You can delete tracks to free up some memory.
Browsing the genome
Changing the position
You can change the position of the displayed window by:
- Dragging any track on the left or on the right with the left button of the mouse
- Clicking with the middle button of the mouse inside a track and then moving the cursor on the left or on the right of the middle red line
- Moving the knob of the position bar on the control panel
- Changing the value of the position text field on the control panel
- Using the keyboard left and right arrows
Changing the chromosomes
You can switch the selected chromosome by:
- Changing the selection in the chromosome box on the control panel
- Changing the text of the position text field on the control panel
Changing the zoom
The level of the zoom can be modified by:
- Wheeling up or down inside a track with the mouse wheel
- Using the zoom bar on the control panel
- Changing the text of the position text field on the control panel
Loading a track
To load a track in any row, right click on the handler of any empty track (the blue part on the left of the track). This opens a menu including options to load the various types of tracks that exist in GenPlay.
Examples of tracks that can be loaded in GenPlay are available for download from the GenPlay Library accessible from the GenPlay.net website.
Loading a variable window track
Variable window tracks allow the visualization of windows of variable sizes with a score associated to these windows.
Select the “Load Variable Window Track” option. This opens up a file chooser dialog box. Load the file of your choice from the list of available fixed window files and click the open button.
Please refer to the File formats section if you want to know what kind of file can be loaded as a variable window track.
Chromosome Selection
After selecting your file, a new window will appear and ask which chromosome to extract. By default all the chromosomes of the project are selected. If you want to change this selection, click on the "modify selection" button and uncheck the undesired chromosomes. Working on fewer chromosomes will save memory and loading time.
Important Note: When specific chromosomes are selected, GenPlay only works accurately if the files that are loaded are sorted by chromosomes. Unsorted files may load incompletely, leading to a loss of valuable information.
Score Calculation
Once the chromosome selection is done, a final window will pop-up and ask you to name the track. The default name is the loaded file name. If there are overlapping windows in your data file, you'll also be prompted to select a method for calculating the score of the windows. Overlapping windows will be split into smaller windows using a simple algorithm.
Loading Fixed Window Track
Fixed window tracks display bin lists. They are useful to represent the results of many types of experiments including, but not limited to: CHIP-seq, RNA seq, and TimEX-seq. Files containing the results of alignments (SAM, bowtie, Eland) and files containing already created bin lists (bed, bgr, etc.) can be loaded using this option. In the case of alignment files, bin lists will be created on the fly as described below. Files containing the results of micro-array experiments can also be loaded as long as they are in one of the accepted formats.
By right clicking on an empty track handler, the contextual menu will pop up. Select the “Load Fixed Window Track” option. This opens up a file chooser dialog box as shown in the figure on the left.
Load the track of your choice from the list of files and click the open button. Please refer to the File formats section if you want to know what kind of file can be loaded as a fixed window track.
Track Name
The default track name will be the file name. The name of the track can also be change later after the track is loaded.
Window Size
This specifies the size of the genomic windows (bins) in base pair (bp) for the track that will be created to summarize the results.
Score Calculation
This option allows you to choose how the scores of the bins are calculated. You may choose between three options: average, maximum or sum. The algorithm of the score calculation is explained below.
Strand Selection
If your input file contains information regarding the strands, you'll be able to choose to load the data from either both or only one strand. You can also decide to shift the reads from both strands as shown in the figure below.
Data precision
Because GenPlay requires a lot of RAM memory, we provide the option of changing the precision at which the score for each bin is stored.
- Scores in 64 bit are stored in floating value double precision (which can represent extremely large numbers unlikely to be useful for genomic experiments).
- Scores in 32 bit are stored in floating value single precision (which can also represent very large numbers).
- Scores stored in 16 bits can range between - 3267.8 and +3267.7 (with one decimal place).
- Scores stored in 8 bits can range between 0 and 255 (with no decimal).
- Score in 1 bit can be equal to zero or 1 (useful to create masks for instance).
We recommend storing scores in 32 or 16 bits.
Chromosome selection
You can load either the whole genome or only specific chromosomes (which saves time and memory).
Important Note: When specific chromosomes are selected, GenPlay only works accurately if the files that are loaded are sorted by chromosomes. Unsorted files may load incompletely, leading to a loss of valuable information.
When the OK button is clicked, the track is loaded in the location desired.
Loading a gene track
After right clicking on the empty track handler, select the “Load Gene Track” option. This opens up a file chooser dialog box that allows you to select the file that you want to load. Please refer to the File formats section if you want to know what kind of file can be loaded as a gene track.
Once it's done, just wait until the loading is complete and the gene track will appear in the track you selected.
Note that the genes on the plus strand are in red and the genes on the minus strand are in blue. If the file contains expression values, the exons are color coded to represent the expression (red = high, blue = low, as shown on the right).
Loading a sequence track
After right clicking on the empty track handler, select the “Load Sequence Track” option. This opens up a file chooser dialog box that allows you to select the file that you want to load. Please refer to the File formats section if you want to know what kind of file can be loaded as a sequence track.
Sequence tracks show DNA sequences from .2bit files.
The hg18, hg19, mm8 and mm9 sequence files can be downloaded from the library of GenPlay.
Loading a SNP track
First, select the “Load SNP Track” option on the track contextual menu. This opens up a file chooser dialog box that allows you to select the file that you want to load. Please refer to the File formats section if you want to know what kind of file can be loaded as a SNP track.
A SNP track shows the Single-Nucleotide Polymorphisms.
Loading a repeat track
Select the “Load Repeat Track” option on the track contextual menu. This opens up a file chooser dialog box that allows you to select the file that you want to load. Please refer to the File formats section if you want to know what kind of file can be loaded as a repeat track.
This track type displays repeats organized by family or class.
Loading data from a DAS server
The distributed annotation system (DAS) is a client-server system in which a client can retrieve data from one or multiple servers. GenPlay can connect to any server that follows the DAS/1 protocol as specified by BioDAS
The “Load from DAS Server” option from the track contextual menu will show the DAS Dialog.
Select the server from which you want to retrieve the data in the "Server" box.
Then select the "Data Source". Most of the time, the Data Source corresponds to the reference genome that you want to work on.
Once that's done you need to select the data that you want to retrieve in the "Data Type" box.
GenPlay can either generate a gene track or a variable window track from the retrieved data. You can select what type of output track you want in the "Generate" option.
Finally, you can also choose to download data on only a part of the genome. This can be useful because retrieving data from a DAS server can be time consuming.
Note: The DAS server section shows how to add new servers to the list of available servers in the DAS dialog.
Generating a Multi Curves Track
If more than one fixed or variable window tracks are loaded, you can overlay them in a multi curves track. To do so, first select the "Generate Multi Curves Track" in the track contextual menu.
Then a dialog will appear asking you which tracks you want to see in the multi curves track.
The available tracks are in the list on the left of the dialog and the selected track appears in the list on the right. Select a track by clicking on its name and use the left and right arrows in the middle of the screen to toggle a track from one list to the other. Double clicking on track produces the same effect.
The order of the tracks in the right list will determine the order in which the tracks are printed. The track on top of the list will be printed on top the other tracks. You can change the order of the tracks by clicking on the name of a track in the right list and using the up and down arrow in the middle of the dialog.
Note: in order to change the appearance of a the multi curve track, you need to change the appearance of the tracks that appear in the multi curves track.
Loading stripes
By clicking on the "Load Stripes" option of the track contextual menu you can load transparent stripes superimposed on a track. The stripes can be useful to show regions of interest such as CPG Islands or repeat regions.
Check the File formats section out if you need to know what kind of file can be loaded as a stripes.
Main Menu
On GenPlay’s main screen click on the top left button (shown by a little hammer and spanner) to pop up the main menu.
Load / Save Project
This menu allow you to load or to save a whole GenPlay project in a really HDD-space efficient binary compressed format. When you load a project of GenPlay all the track of your current project will be replaced by the one from the project you loaded and all the information that hadn't be saved will be lost. Important Note: The GenPlay project files may be dependent to the version of GenPlay you're using. Be sure to remember with which version of GenPlay you saved a project and use the same version next time you load your project.
Full Screen
Click on this item of the main menu to toggle the full screen mode. When the full screen mode is on, the control panel and the status bar are hidden. You can also toggle the full screen mode by pressing the F11 key.
Option
The option menu item allows you to modify the configuration of GenPlay. Please refer to the section Changing the configuration of GenPlay for further information.
RNA To DNA Reference
Help and About GenPlay
The help and the about GenPlay options open a browser showing respectively the documentation and about pages of GenPlay website.
Exit
This option closes the application after asking for confirmation.
Changing the configuration of GenPlay
Click on the option item of the main menu to open the configuration screen.
General options
The following screen let you set the general options:
The Default Directory lets you specify where the files containing GenPlay tracks will be stored in your file system.
The Log File is a text file that contains a time-stamped history of the files extracted and loaded on GenPlay.
From this screen, you can also modify the appearance of the software by changing the look&feel.
Configuration files
The configuration files screen allows the user to change the zoom file as well as the genome configuration file. It is necessary to restart GenPlay after modifying this option in order to take them into account.
Zoom file
The Zoom configuration file is a file that contains the predefined levels of zooming. To change this levels of zooming just create a text file with one level of zooming (in bp) per line order from the smallest to the greatest. Here is an exemple:
10 100 1000 10000 100000 1000000 10000000 100000000
Genome file
Once GenPlay is started a configuration file describing the genome that you want to analyze (the default is human hg19). Configurations are simple text file that specify the name and length of the chromosome or scaffold of the current genome. Configuration files for human and mouse recent assembly can be downloaded from the GenPlay library accessible from the GenPlay.net web page (please see below). Configuration files for any genome can easily be created in any word processor using the provided examples as a model. Here is an example of genome file:
chr1 249250621 chr5 180915260 chr13 115169878 chrX 155270560 chrY 59373566
Track option
The Number of Tracks text box defines the maximum number of tracks that can be loaded on GenPlay.
The Default Track Height text box defines the height of each of the tracks.
The Undo Count text box defines the number of operations that can be undone. Note that the higher the number of undo you select, the more memory will be required.
DAS server
The DAS server option shows the list of existing DAS servers along with the URL where these servers are located. It also provides options to add new servers and remove existing servers.
GenPlay can communicate and retrieve data from the servers implementing the DAS/1 protocol
Restore default
The Restore Default configuration restores everything back to the factory settings.
File formats
The different file formats used in GenPlay are described on this page.
Manipulating tracks
Moving a track
To move a track up or down in the track list, just click on the track handler (the left part of the track with the track number) and drag the track to the desired position.
Inserting a track
To insert a track, right click on the trach handler of the track right under where you want to insert your track and choose the "Insert" option.