Genome coverage

[jjk]

I used bowtie to create sam files that are loaded in a tablet program for chloroplast assembly by tags. I guess there is an overall coverage of about 80%. But is there a way to let the program calculate the precise coverage by the tags in comparison to the chloroplast sequence?

Thx

[dawe]

You may check BEDTools. There's a coverageBed utility. Of course, you must convert sam to bed first!
d

[andrehorta]

Hi!

Are you using Linux or Windows. I can help you!

André

[zhlu1986]

how to use coverageBed

How to use coverageBed to caculate the coverage of reads to reference?
I have changed sam to bam and then to bed.
I've got only one sam files after aln reads to reference.
Why does the coveragebed programme need to bed files a and b like this:
coverageBed [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>
If this method does not work.
Is there any other software or script to caculate assembled contigs' coverage to reference?

ps.
the assemble programme is not the popular ones

[chariko]

Maybe this thread may help you.

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

[zhlu1986]

Maybe this thread may help you.

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

Thank you .chariko
But I want this kind of results:

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%

[Michael.James.Clark]

Read the documentation for BEDtools, it gives an example of how to do this exactly. Very nice PDF on their website!

It doesn't require the first input to be a bed file, either. It can be a BAM file. See the -abam option.