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  • Matt.Ralston
    Member
    • Jan 2014
    • 10

    #1

    Does each read in a paired-end SAM file get the 0x0001 flag?

    Hello everyone, I have a simple, generic, question about SAM format flags in paired-end Illumina data. Does every read in a SAM file from a paired-end sequencing run automatically have the 0x0001 flag?

    Thanks!
  • Brian Bushnell
    Super Moderator
    • Jan 2014
    • 2709

    #2
    Originally posted by Matt.Ralston View Post
    Hello everyone, I have a simple, generic, question about SAM format flags in paired-end Illumina data. Does every read in a SAM file from a paired-end sequencing run automatically have the 0x0001 flag?

    Thanks!
    Yes. Normally it's referred to as "0x1".

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