What Do The Columns Of "Junctions.Bed" File Mean?

Question

[Sameet]

Hi,

I have seen the junctions.bed file created everytime I run tophat. I tried reading through the manual, but I could not find a satisfactory explanation for all of the columns in this file.

Is there any resource where this description is available in detail.

Answer 1

[cpcantalapiedra]

junctions.bed. A UCSC BED track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction.

If you go to UCSC BED format http://genome.ucsc.edu/FAQ/FAQformat.html#format1