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Old 04-02-2013, 01:43 PM   #1
Location: USA

Join Date: Dec 2011
Posts: 45
Default RNA-Seq alignment issue

Hello all,

I have been given paired-end RNA-Seq files to align against a couple of references. I used Bowtie2 to do the job. The alignment results were very low in most of the cases (less than 5% overall alignment rate).Now, we are thinking this might be caused by either contamination or mix up samples.

Any suggestion what to do in such case?
Thank you in advance
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