Question: understanding bedtools coverage output
0
gravatar for vinayjrao
3.4 years ago by
vinayjrao180
inStem, India
vinayjrao180 wrote:

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 :)

rna-seq bedtools • 4.7k views
ADD COMMENTlink modified 3.4 years ago by t_stranger40 • written 3.4 years ago by vinayjrao180

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

ADD REPLYlink written 3.4 years ago by cpad011214k
1
gravatar for t_stranger
3.4 years ago by
t_stranger40
t_stranger40 wrote:

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.

ADD COMMENTlink written 3.4 years ago by t_stranger40

Column 9 makes more sense now. Thank you

ADD REPLYlink written 3.4 years ago by vinayjrao180
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