JBrowse 2

Step 1: Load BAM files representing tumor and normal sequencing data.

Step 2: Load VCF files containing somatic mutations.

Step 3: Load segmentation files representing copy number alterations.

Step 4: Visualize all the data tracks together in the JBrowse 2 linear view to identify regions of interest.

Step 1: Load VCF or BEDPE files containing SV calls.

Step 2: Use the synteny view to compare the SVs across different samples or populations.

Step 3: Use the circular view to visualize large-scale genomic rearrangements.

Step 4: Integrate SV data with gene annotation tracks to assess the impact on gene function.

Step 1: Load BigWig files representing gene expression levels from RNA-seq data.

Step 2: Load VCF files containing genomic variants.

Step 3: Visualize gene expression tracks alongside variant tracks in the linear view.

Step 4: Identify variants that correlate with changes in gene expression levels.

Step 1: Load genome assemblies for multiple species into JBrowse 2.

Step 2: Use the synteny view to visualize conserved regions between genomes.

Step 3: Load annotation tracks for each species, such as gene models and regulatory elements.

Step 4: Compare the annotation tracks to identify conserved genes and regulatory regions.

Step 1: Load BAM files representing sequencing data from CRISPR-edited cells.

Step 2: Load BED files containing predicted off-target sites.

Step 3: Visualize the sequencing data and off-target sites in JBrowse 2.

Step 4: Identify indels and other mutations at the on-target and off-target sites.