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  • struggler
    Member
    • May 2012
    • 12
    #1

    Bowtie2 mapping message: [samopen] SAM header is present:

    Dear All,

    I am using Bowtie2 to map Illumina Hiseq reads to a reference genome and getting the following message:

    [samopen] SAM header is present: 528 sequences

    I don't know if this is a trivial issue or some significant error. I have tried searching details of this message but can't find any information on what does this '[samopen] SAM header is present:' line means and would highly appreciate some feedback on this message.

    Regards,
    S
    Tags: None
    • maubp
      Peter (Biopython etc)
      • Jul 2009
      • 1544
      #2
      It is a harmless bit of diagnostic information from samtools, but I would worry if your reference genome does not have 528 sequences.

        Comment

        • struggler
          Member
          • May 2012
          • 12
          #3
          Many thanks! Your reply is spot on as indeed the reference genome contains 528 fasta headers.

          Regards,
          S

            Comment

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