OptionsExample | This command allows a user to bring the IGB window to the forefront of the screen, in front of all open windows. It accepts no arguments. | bringToFront | deleteAllTracks | | This command accepts no arguments, and will remove all loaded data sets from IGB on execution (note: including default annotation tracks for a genome version). | deleteAllTracks |
deleteTrack | <file or URL> | This command accepts one or more comma separated files identified by full path or URL. If a matching track is found for the specifed URL/path it will be deleted. | deleteTrack http://igbquickload.org/A_thaliana_Jun_2009/TAIR10_mRNA.bed.gz |
genome | <version> | Specify a genome version none | Make IGB the top window on the Desktop. | bringToFront |
genome | <version> | Load a genome version. Accepts IGB-friendly genome version names (e.g., H_sapiens_ |
Mar2006. Any genome version or synonym that's accepted by IGB is accepted here.and synonyms. | genome H_sapiens_Mar_2006 |
goto | <region> | Go to a region |
of a chromosome (e.g., "chr1:40000-60000"). Any format that's accepted by IGB is accepted here. Commas are optional. | goto chr1:13,640,211-13,643,760 goto chr1:13640211-13643760
|
hidetrack | <file or URL> | Hide the |
specified homescreenIGB Start Screen. | homescreen |
load | <file or URL> | Load the specified file (identified by full path) or URL into IGB. The data set will appear in the |
user's loadfromserver | | This command allows a data set to be loaded from a configured "Data Source Provider" (e.g. a Quickload site). This command requires a server URL and a datasource URL.loadfromserver http://igbquickload.org/ http://igbquickload.org/A_thaliana_Jun_2009/TAIR10_TE.bed.gz | loadmode | <NO_LOAD | REGION_IN_VIEW |
| CHROMOSOME | GENOME> <file or URL> | Change the load mode for |
the specified data set or file, identified by full patha data set. Note: The loadmode command will work for any loaded track. Make sure to load your desired track before calling the loadmode command. | loadmode GENOME http://igbquickload.org/M_musculus_Dec_2011/M_musculus_Dec_2011_refGene.bed.gz |
loadsequence | none | This is equivalent to clicking the Load Sequence button in IGB. This triggers loading of the reference sequence for the region in view. | loadsequence |
refresh |
none | This is equivalent to clicking the Load Data button in IGB. This triggers loading of data from the active data sets available in IGB, as specified in the load command. | refresh |
select | <geneids> | Selects the given gene IDs, which are passed in as a comma-separated list. If the command contains a single gene ID then IGB will select and jump-zoom to the given gene. | select AT1G36280.2,AT1G36240.1,AT1G36340.1 |
selectfeature | <geneids> | Selects the given gene IDs, which are passed in as a comma-separated list. | selectfeature |
showtrack | <file or URL> | Unhide the specified track. Accepts one or more comma separated files identified by full path or URL. | showtrack http://igbquickload.org/O_sativa_japonica_Oct_2011/O_sativa_japonica_Oct_2011.bed.gz |
sleep | <milliseconds> | Sleep the application for x milliseconds. | sleep 6000 |
snapshot | <filename> |
Export Note: specify the full path to file.
| Create an image showing the entire IGB window. the entire frame an image file. The filename extension determines the format. Supported formats are .png, .jpeg, and .svg |
. . Note: This command only works on Mac and Linux if attempting to export an SVG file. | snapshot alternativesplicing1.png |
snapshotmainView | <filename> |
Export the main view an image file. The filename extension determines the format. Supported formats are .png, .jpeg, and .svg. Same as snapshot but only makes an image showing the main IGB data display. | snapshotmainView testimage.jpeg |
snapshotmainViewWithLabels | <filename> | Export the main view with labels an image file. The filename extension determines the format. Supported formats are .png, .jpeg, and .svg. | snapshotmainViewWithLabels imageexport1.svg |
snapshotslicedViewWithLabels | <filename> | Export the sliced view an image file. The filename extension determines the format. Supported formats are .png, .jpeg, and .svg. | snapshotslicedViewWithLabels April_1_2015.png |
snapshotwholeFrame | <filename> | Export the entire frame to an image file. The filename extension determines the format. Supported formats are .png, .jpeg, and .svg |
. . Note: This command only works on Mac and Linux if attempting to export an SVG file. | snapshotwholeFrame GeneAT1G36280wholeframe.jpeg |
unload | <file or URL> | If a matching track is found for the specified URL/path it will be deleted. Accepts one or more comma separated files identified by full path or URL. | unload http://www.igbquickload.org/rnaseq/A_thaliana_Jun_2009 |
/cold_stress/cold_control.sm