JunctionBED - nsalomonis/altanalyze GitHub Wiki
Below is the column format used in the junction-level BED file recognized by AltAnalyze. When a .bed file containing these 12 fields is imported, AltAnalyze will assume the data are detected junctions from your experiment. This can be RNA-seq or even an unsupported microarray. Default expression is non-log read counts but can be log2 (select format as log in AltAnalyze). The notes field can include any or no information.
| chr | position1 | position2 | notes | expression | strand | |
|---|---|---|---|---|---|---|
| chr19 | 3266448 | 3267268 | JUNC00000001 | 2 | - | ... |
| start | stop | null | null | exon lengths | null | |
|---|---|---|---|---|---|---|
| ... | 3266448 | 3267268 | 255,0,0 | 2 | 11,27 | 0,793 |
When the read is on the positive strand:
- 5' splice-site: position1+length1
- 3' splice-site: position2-length2+1
When the read is on the negative strand:
- 5' splice-site: position2-length2+1
- 3' splice-site: position1+length1