Total number of junctions in junctions.bed generated by TopHat

Question

[justinkablan225]

Hello, I run TopHat alignment on my RNA-Seq data and get some results within junctions.bed. This is an abstract that I want to understand for interpretations. I want to know the total number of junctions and the number of Found junctions and other explanations that go with it. Thanks lot.

track name=junctions description="TopHat junctions"
1   15010   15826   JUNC00000001    3   -   15010   15826   255,0,0 2   28,31   0,785
1   15920   16627   JUNC00000002    3   -   15920   16627   255,0,0 2   27,21   0,686
1   16735   16870   JUNC00000003    3   -   16735   16870   255,0,0 2   30,13   0,122
1   17020   17254   JUNC00000004    7   -   17020   17254   255,0,0 2   35,22   0,212
1   17346   17623   JUNC00000005    3   -   17346   17623   255,0,0 2   22,18   0,259
1   17723   17948   JUNC00000006    3   -   17723   17948   255,0,0 2   19,34   0,191
1   18027   18301   JUNC00000007    7   -   18027   18301   255,0,0 2   34,34   0,240
1   169237  172567  JUNC00000008    1   -   169237  172567  255,0,0 2   27,11   0,3319
1   185313  185524  JUNC00000009    5   -   185313  185524  255,0,0 2   37,34   0,177

[lieven.sterck]

not sure if I understand but for the total number of junctions found you need to count the numbers of rows in that file (minus the header line ) .

I don't get what you mean by number of junctions vs found junctions ?

[justinkablan225]

Thanks, it's one thing that I want.  
I  see in literature that authors report  ``Loaded junctions'' and ``Found junctions" in their case. 
I want to find those informations that concern my analysis. 
Alignment was done with hg38 human genome.

[Kevin Blighe]

Check the materials and methods to see how they define "loaded" versus "found". If you want, provide such a manuscript.