|Show segmented coverage:|
|Divide coverage by:|
|Publication style plot|
|Minimum variant size:|
|Minimum split reads:|
|Minimum discordant pairs:|
|Minimum miscellaneous read evidence:|
|Download coverage data (.csv)|
|Download variant data (.csv)|
(change database in Genes tab under annotation)
Ribbon (genomeribbon.com) is a long-read alignment viewer that allows you to see all the reads mapping near a variant including their other alignments across the genome, and you can see detailed alignments for each read to determine which parts of the read are mapping where.
|Distance threshold for CNV matching and nearby variant count:|
|Distance threshold for reciprocal pair of variants:|
Showing variants out of . Unfiltered, there are variants
Filter in text boxes by =,>, or <, and click column names to sort. Click on a row in the table to see that variant in the visualizer
Enter gene names
Start typing a gene name into the input box and click on the gene you want (or use the arrow genes to walk up and down the list and press enter on the gene you want). Select two genes and then click the Submit button to search the rearrangement graph for a connection between the two genes.
Upload a list
Upload a list of gene fusions
The file should have a pair of genes on each line separated by tabs, commas, or spaces, with the gene names in the first two columns matching the annotation.
Shortest paths found:
Click on a row in the table to jump to each gene fusion in the visualizer. "distance" is the number of basepairs in the path between the two genes. "num_variants" indicates the number of variants this path threads through in the graph. "path_chromosomes" shows all the chromosomes found along the path. If the genes have a direct connection that intersects both genes, the distance will be 0, num_variants will be 1, and path_chromosomes will be only the chromosomes the genes themselves reside on.
|Max bp distance to search:|
Number of starting points:
Number of target end-points:
Calculate distances across the graph
Use the tables in the "From" and "To" panels above to filter down to the intervals you want to search between. Then click "Calculate" to get a result for each interval in "From", finding its closest interval among all the possible intervals in the "To" table.
Click on one of the results in the table to show the path in the visualizer.
Found results for X out of N total intervals in the "From" table. Showing at most 30, but filter and sort works on the whole set (as with all tables in SplitThreader).
Upload a bed file
Upload a bed file of features
Upload a bed file containing features to calculate distances between any sets of features and genes.
Switch chromosomes by dragging chromosome names from the circos plot onto either the top or bottom coverage bar charts to switch that plot to the new chromosome.
Zoom by double-clicking the coverage bar charts and move around by dragging when you are zoomed in. Also click the + and - buttons to zoom in and out.