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Old 04-22-2011, 02:04 PM   #1
unidodo
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Default not uniquely mapped reads

We got a large fraction (70%) of not uniquely mapped reads. Just wondering if anyone knows the possible cause?

Thanks in advance.
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Old 04-22-2011, 02:27 PM   #2
nilshomer
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What experiment, what technology? Please be verbose in your answer!
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Old 04-22-2011, 03:07 PM   #3
unidodo
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Thanks, nilshomer!

RNA-seq using HiSeq.

Seems that majority of not uniquely mapped reads come from either one chromosome or mitochondrion genome.
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