Question: "deletions.bed" file of tophat2 output' s mean.
0
gravatar for leenaehyeon
3.6 years ago by
leenaehyeon10
Korea, Republic Of
leenaehyeon10 wrote:

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

 

 ex)

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

help ..

rna-seq • 1.2k views
ADD COMMENTlink modified 3.6 years ago by glihm590 • written 3.6 years ago by leenaehyeon10
1
gravatar for glihm
3.6 years ago by
glihm590
France
glihm590 wrote:

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.

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by glihm590
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