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.

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