Table Description
Above the table is a search bar which can be to seach the ID's
Each insertion is identified by its insertion site in genomic coordinates with the following format:
<chromosome>:<coordinate>
This column will only be in the table if the --genes argument is provided to the alignment step.
Currently TranspoScope makes use of the refFlat.txt annotion file for identifying the nearest gene. This file will generally be included with the reference genome, but it is also possible to download the refFlat.txt file from the UCSC genome portal (hg19, hg38).
The gene name is colored red when the insertion is found within the exon of the gene. The gene name is colored orange when the insertion is found within the intronic regeion
When the insertion falls outside of a gene the nearest gene is displayed and the color demonstrates the distance from that gene. The colors range from green (closer) to blue (further).
| Distance | Color |
|---|---|
| Exon | |
| Intron | |
| 1 - 300 bps | |
| 301 - 1000 bps | |
| 1001 - 3000 bps | |
| 3001 - 10000 bps | |
| > 10001 bps |
When using TIPseqHunter this column is named Pr and the values represent the probability that this is a real insertion defined by TIPseqHunter. When using MELT this column is named Assess and displays the 'Assess' metric output by melt for the insertion