I've alignment using Tophat2, and got ".bed"files, including deletions.bed, insertion.bed, junctions.bed.
and I opened the "deletions.bed"file.
there are 4 columns
track name=deletions description="TopHat deletions"
chr1 16917 16919 - 1
chr1 18869 18871 - 3
chr1 24347 24349 - 3
What is it in the 4th,5th column??? I don't know that means.
I think 1st column is chromosome , 2nd & 3rd column means where the deletion takes place,
4th is I don't know, 5th is how many deletions ??
3rd - 2nd != 5th