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  • Transfer a whole genome with .bam format

    Dear all,

    Do you have experience to transfer a whole genome of short-reads with ~35X sequenced by Illumina GA to .bam format using samtools? I feel very strange when I got more than 500G data. I addition, how can you extract chromosomes one by one and sort as well as index them? Thank you very much!

    Wuhoucdc

  • #2
    Originally posted by wuhoucdc View Post
    Dear all,

    Do you have experience to transfer a whole genome of short-reads with ~35X sequenced by Illumina GA to .bam format using samtools? I feel very strange when I got more than 500G data. I addition, how can you extract chromosomes one by one and sort as well as index them? Thank you very much!

    Wuhoucdc
    Never had a whole genome with that coverage :-( Sorted BAM may be slightly smaller.
    To extract a single chrom (or a single region) index it

    Code:
    samtools index file.bam
    and then extract your region

    Code:
    samtools view file.bam chrom[:start-end]
    HTH

    d

    Comment


    • #3
      Thanks for your answer, dawe.

      But why did you say "Never had a whole genome with that coverage "? Most of the sequenced individuals such as YH (PMID:18987735) and AK1 (PMID:19587683) were higher than that coverage (>35X).

      Wuhoucdc
      Last edited by wuhoucdc; 08-22-2010, 01:03 PM.

      Comment


      • #4
        Originally posted by wuhoucdc View Post
        Thanks for your answer, dawe.

        But why did you say "Never had a whole genome with that coverage "? Most of the sequenced individuals such as YH (PMID:18987735) and AK1 (PMID:19587683) were higher than that coverage (>35X).

        Wuhoucdc
        :-) I usually deal with ChIP-seq or exome analysis, never had a "first hand" high coverage of human genome.
        d

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