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Old 03-05-2014, 08:36 AM   #4
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Location: Chicago

Join Date: Mar 2014
Posts: 3

Originally Posted by edm1 View Post
Does 45.3% success rate seem close to what I should be expecting in mice? I have nothing to compare it to.
Hey edm1,

I'm not sure if you were ever able to get advice on whether 45.3% is close to what you should expect, but here are my two cents:
1) The "alignment_not_unique" feature is for reads with low alignment quality, which usually means reads that had multiple mappings. Count-based methods of differential expression (e.g. DESeq) usually ignore these, i.e. they focus on "unique matches", so you shouldn't include them in your final percentage tally. Excluding them gives you a success rate of 62.8%.
2) I'm not very familiar with the literature on what an expected success rate would be, but one example I am aware of (and was posted in another forum) is this nature paper (link:, reporting in their supplementary information that they mapped an average of 86% (range of 64-91%) uniquely matching reads to exons. All of their numbers are reported in the first supplementary table. Thus, your success rate of 62.8% is close to the bottom of their range. There might still be some areas of improvement for you, but you're pretty darn close.

Hope that helps!
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