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Old 05-24-2016, 11:58 AM   #6
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Location: Bay Area

Join Date: Jun 2012
Posts: 118

This wouldn't explain why your FPKMs are zero for every gene, but your alignment statistics are a little alarming.
Aligned pairs: 10988017
of these: 6368400 (58.0%) have multiple alignments
That's a really high multiple alignment rate for mouse RNA-Seq. I've only ever seen it that high when the rRNA depletion/ polyA selection failed. Even so, with 10M reads, you should be picking up >10k genes. How were these samples prepared?
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