A video demonstration of the TranspoScope.
TranspoScope is a biologist-friendly system for rapidly assessing the validity of potential retrotransposon insertions. A quick visual picture of the read pairs supporting each insertion A special pane to evaluate the quality and quantity of junction reads, which we perceive as most critical for confidently calling an insertion A zoomable format that allows a user to zoom from a multi-kilobase view for looking at peaks to a nucleotide level view for inspecting individual nucleotides e.g. in the junction sequence itself, and also to assess the quality of each critical nucleotide A pane reporting on the nearest gene(s) and if intragenic, the position within the gene and finally Link to the UCSC genome browser using the coordinates of the selected site
This application is meant to accomplish the following objectives:
In addition, the instances of restriction enzyme sites used in the TIPseq experiment that
lie near the insertion point are indicated as red vertical lines.
The histogram colors are determined by the orientation of the the read pairs relative to the junction region.
Drag the histograms in the above image to see how the colors are affected by the orientation of the reads.
Red lines are used to show enzyme cut sites.
When the mouse pointer is hovered over one of the enzyme cut sites a tooltip will be shown providing the enzyme name as well as the location relative to the insertion site.
The junction region is the blue shaded area shown between the two blue guide lines.
Junction Reads are accessed by clicking on the 'Junction Reads' button located above the chart.
Junction Reads are reads which fall accross the junction region.
Letters are colored to indicate indels as well as soft-clipping:
ACGTN : Match
ACTGN : Insertion
----- : Deletion
ACTGN : Soft Clipping
One insertion site is shown per row in the table.
ID : Shows the chromosome and genetic coordinates of the insertion site. The number in the brackets indicates the width of the junction region. Gene : UCSC refseq annotation is used to annotate the insertion.
Located in an Exon
Located in an Intron
Closest Gene ≤ 299bp away
300bp ≤ Closest Gene ≤ 999bp
1000bp ≤ Closest Gene ≤ 2999bp
3000bp ≤ Closest Gene ≤ 9999bp
Closest Gene ≥ 10000bp away
P : Probability of the insertion being a true insertion. UCSC : Link to UCSC genome browser with a custom track showing the junction region.