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  • 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?

    Thx

  • #2
    You may check BEDTools. There's a coverageBed utility. Of course, you must convert sam to bed first!
    d

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    • #3
      Hi!

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

      André

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      • #4
        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

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        • #5
          Maybe this thread may help you.

          Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

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          • #6
            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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            • #7
              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]
              Projects: U87MG whole genome sequence [Website] [Paper]

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