multiple alignment?
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Shicheng Guo
Samtools tview : what does underlined reads mean ? Secondary or Orphan
I don't understand in samtools tview the signification of an underlined read.
I understand what orphan means (in paired end, the other pair end is not mapped), but what secondary means? it means it's a duplicate ? Sometimes I can have two reads with the same name underlined and I don't know how to analyze them.
I found Here somebody talking about tview legend but it's not clearly explain for underlined reads.
Thanks
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Secondary: the read was mapped elsewhere (primary location). This position is another candidate position for this read.
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Pierre Lindenbaum
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