Example Junction BED Format

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