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Old 04-17-2018, 05:12 PM   #3
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 823
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I'd recommend doing an analysis on the unmapped reads to make sure that they are not hitting something other than your intended target. With a tumour sample it's unlikely to be a contamination issue, but just in case, you could feed the unmapped reads through Centrifuge or OneCodex just to be sure of that.
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