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  • blu78
    Member
    • Apr 2010
    • 20
    #1

    SAM format NH tag question

    Hi guys,

    I have a quick question about SAM format and the NH tag.

    From the Format specs: NH should contain "Number of reported alignments that contain the query in the current record"

    What is it meant by "in the current record"?

    I am aligning reads from a single ends file and I see that the same read aligns in more than one position (even on different contigs) and in the NH tag of the different alignments I get sometimes different values.

    How is this possible?

    Thanks in advance
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