how to caculate coverage

[zhlu1986]

I have assembled reads to contigs and then map it to referece.
I got a sam file.
How to caculate the coverage of it?

I want to caculate the rate, for example:
the length of reference is 10000bp
the length of reads mapped reagion is 2000bp in all
and the coverage rate is 20%

Is there any script or software?
Thank you all.

[boetsie]

Have a look at my older thread, it might help you;

http://seqanswers.com/forums/showthread.php?t=7679

[zhlu1986]

Thank you, boetsie.
But my purpose is different from you .
I want to caculate the rate, for example:
the length of reference is 10000bp
the length of reads mapped reagion is 2000bp in all
and the coverage rate is 20%

[maubp]

Do you want the percentage of the reference covered by at least one read?