"deletions.bed" file of tophat2 output' s mean.

Question

[leenaehyeon]

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 in the 4th and 5th columns? 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

Please help

Answer 1

[glihm]

Here, you have the documentation about this (scroll at the bottom of the page). ;)

The 4th column is the strand. (" - " or " + ").

The 5th is a score. You do not have to try 3rd - 2nd, it makes no sense.