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Old 05-12-2010, 05:07 AM   #1
Location: italy

Join Date: Apr 2010
Posts: 20
Default 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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