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Old 12-10-2009, 07:06 PM   #1
Location: Brisbane

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Default Genome coverage

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?

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Old 12-11-2009, 12:18 AM   #2
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You may check BEDTools. There's a coverageBed utility. Of course, you must convert sam to bed first!
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Old 01-12-2011, 04:28 AM   #3
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Are you using Linux or Windows. I can help you!

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Old 04-13-2011, 02:12 AM   #4
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Default 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?

the assemble programme is not the popular ones
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Old 04-13-2011, 05:56 AM   #5
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Maybe this thread may help you.
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Old 04-13-2011, 05:10 PM   #6
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Originally Posted by chariko View Post
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%
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Old 04-13-2011, 05:32 PM   #7
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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.
Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
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bowtie, coverage, genome, sam

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