Visualization is immediately accessible for cases that have been analyzed from FASTQ or BAM files. If the analysis was performed from VCF files, mapping visualization can be enabled using local BAM files.
a. Creating a case via API with location of alignment files* defined in JSON;
b. Loading local alignment files* to your case in Emedgene.
Click on the button in the top right corner of the section and select relevant BAM and BAI files stored on your PC. After that, you will be able to select the samples to be shown in the viewer by selecting the corresponding sample names on top of the section.
BAM and BAI (or CRAM and CRAI)
While navigating between variants in the emedgene platform, there is an option to change the genomic position in the full-featured IGV desktop application according to the currently selected variant. How cool is that?
In order to enable or disable control of IGV from a web browser, please open your desktop IGV application and follow the instructions:
Go to the View menu and select Preferences.
Go to the Advanced tab.
Select or unselect the Enable port option to enable or disable the feature, respectively.
Save the changes.
That's it!
You can thoroughly review mapping visualization in desktop IGV, while interpreting the variant in emedgene. Moving between variants in the emedgene platform will also change the position on your desktop IGV.
Load to IGV is available for:
FASTQ cases;
VCF cases sent through API with alignment files* connected.
Make sure that control from a web browser is in the desktop IGV.
Make sure that IGV integration is enabled in the of the Variant page sidebar.
Open an IGV instance on your computer.
In the top right corner of the section, click Load to IGV to send alignment files* to IGV, which will automatically show the genomic region flanking the variant under review.
BAM and BAI (or CRAM and CRAI)
