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Old 08-14-2014, 07:12 PM   #1
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Location: Raleigh-Durham, USA

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Default exosome rna-seq - poor genome aignment

I have exosome rna-seq data with ~13M reads. The data is 50bp single-end from HiSeq 2000 machine. Nugen ovation kit v2 was used for library preparation from total RNA. I aligned the reads to the human genome after quality trimming and got <1% of the reads aligned to the genome. I checked statistics on the sequenced reads and noticed that 90% of the reads were duplicated. Could this be the issue? I appreciate your insights on what might be the issue.
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exosome, genome alignment, rna-seq

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