bed files of TopHat2 output

Question

[Yizhao]

Hi,

I've completed alignment with Tophat2, and got some output files, including deletions.bed, junctions.bed and insertions.bed. My problem is how to tell what info it is in each file. I've checked the instruction of UCSC BED file, but I still cannot make it clear. My deletions.bed file content is like:

---

track name=deletions description="TopHat deletions"
AGTP01133720.1    1571    1573    -    1
AGTP01133720.1    3360    3362    -    1
AGTP01133720.1    14859    14860    -    1
AGTP01133720.1    15434    15435    -    1
AGTP01133720.1    19755    19756    -    1
AGTP01133720.1    20696    20697    -    2
AGTP01133720.1    22781    22782    -    1
AGTP01133720.1    23171    23172    -    1

---

So, what is it in the 1st column? Any explanation will be appreciated.

Answer 1

[iraun]

Hi leo,

I don't know if I understand correctly your question but, in the first column you have the chromosome (scaffold, or contig), where the deletion takes place.

[Yizhao]

I got it. Thx a lot:p

[jc.szamosi]

I guess I have a more basic question than this: What are the deletions? Like, what in the genome do they represent? Are they reads that mapped but the read had a deletion relative to the reference?