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  • novabc
    Junior Member
    • Dec 2010
    • 4
    #1

    export2sam.pl problem

    Hi:

    I used export2sam.pl on export file created by CASAVA 1.7.0. However the generated sam file does not have @SQ lines, and had problem when used with samtools view etc.

    export2sam.pl --read1=test_export.txt > test.sam
    samtools view -h -S test.sam

    Output is:
    [samopen] no @SQ lines in the header.
    [sam_read1] missing header? Abort!

    Any suggestions? Thanks.

    Jason
    Tags: None
  • maubp
    Peter (Biopython etc)
    • Jul 2009
    • 1544
    #2
    Does the samtools -t option to specify the reference FASTA file help?

    Comment

    • novabc
      Junior Member
      • Dec 2010
      • 4
      #3
      Yes, adding -t option works. Thanks.

      Comment

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