JunctionBED

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