understanding bedtools coverage output

Question

[vinayjrao]

Hi,

I'm working with some RNA-Seq data, and I have created my bed files. When I run bedtools coverage, the output has 16 columns. I looked for help on these columns, and all I got was -

1. Chr

2. Chr Start

3. Chr End

4. Read Name

5. Mapping Quality

6. Strand

7. Thick Start

8. Thick End

9. Item RGB

10. Block Count

11. Block Sizes

12. Block Start

13. Coverage Depth

14. Number of Bases at Depth

15. Size of A

16. Percentage of A at Depth

Could someone please explain to me columns 9, 13, 14, 15 and 16 in greater detail?

TIA :)

[cpad0112]

http://www.ensembl.org/info/website/upload/bed.html#optional

Answer 1

[t_stranger]

column 9: RGB is the color that will show in the genome browser, every single color have its own code. Let's say (255, 0, 0) , it will show red color. column 13: Coverage Depth is how many reads in that particular nucleotide sequences. column 15 and 16 I seldom use, wait others to answer.

[vinayjrao]

Column 9 makes more sense now. Thank you