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  • Counting number of short-read cover positions

    Hi everyone,
    I used this command to count the number of short-read cover a position:
    Code:
    samtools view data.bam 20:1000-1000 -c
    If I run this command several time, it would be very slow.
    Is there any way to count the number of short-read cover millions of positions.
    Thank you in advance!

  • #2
    GATK's DepthOfCoverage can do this. Use the -L argument to specify which positions you want coverage information for. http://www.broadinstitute.org/gatk/g...fCoverage.html

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    • #3
      Hi, if you purpose is to get the coverage and visualize them, an easy to use and powerful tool is ngs.plot. It can accept a BED file or use its pre-compiled database and calculate the coverage for any bam file. It then visualize them either as an averaged profile plot or a heatmap.

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      • #4
        Hi d_t_nguyen,

        You may try the featureCounts program included in the Subread package (http://subread.sourceforge.net/).

        Here is the steps to use featureCounts to count your reads. Firstly, create a tab-delimited annotation file like this:

        GeneID Chr Start End Strand
        1 chr20 1000 1000 +
        2 chr20 2000 2000 +


        Then, issue the following command to count reads:

        featureCounts -F SAF -f -O -a your_annotation.txt -i your_sam_file.sam -o results.txt

        The counting results will be saved into file 'results.txt'.

        Alternatively, you may provide a GTF format annotation for summarization. You may also use -T argument to run on multiple threads. Type 'featureCounts' for more information, or have a look at the userguide (http://bioinf.wehi.edu.au/subread-pa...UsersGuide.pdf)

        Best wishes,

        Wei

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        • #5
          Thank you all. I've just realized that pileup format of SAMTools have all I need. I used this command and I had all I want:
          samtools mpileup individual.bam > read.txt

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