Tophat2 deletions.bed output question

[rnastar]

Hi all,

Just a quick question for you: in Tophat's deletions.bed file, what does the last column in the file indicate? The tophat manual does not have much on this. Also, how is it possible that every single deletion in the file is only 1bp? Example is below:

track name=deletions description="TopHat deletions"
chr1	10185	10186	-	1
chr1	14828	14829	-	2
chr1	15879	15880	-	1
chr1	31719	31720	-	4
chr1	36351	36352	-	3
chr1	38728	38729	-	5
chr1	39751	39752	-	1
chr1	51864	51865	-	1
chr1	59253	59254	-	1

Thank you all again for your help!

[kubu4]

Bump. Wondering if this question was ever answered.

[drdna]

Depth of coverage

[Artur Jaroszewicz]

Just a guess: maybe the last column is the number of bases deleted, and the second and third columns are just where it starts?

[drdna]

Nope, it's read coverage. Column two indicates position of first deleted base, column three indicates position of first retained base on other side of deletion.

[kubu4]

Thanks for the info.

Do you have a source for that column representing coverage (makes the most sense) or have you noticed this simply through working with TopHat?

[drdna]

The official header for that column is "score." It only makes sense that this represents coverage. One could always run samtools mpileup on the relevant .bam file to check.