I have an RNASeq sample with mouse data that started with a very low amount of RNA. We did a test run on the MiSeq, trimmed the reads to 75bp, and ran it through TopHat just to see how it's looking.
For the most part it seems fine (no bias to 3' end of genes, 75% mapping rate (low but not terrible)), but then of the aligned reads, 26% are discordant, leaving me with a total overall concordant mapping rate of 50%. Is this okay? What could cause this high-ish discordance rate, and should I worry about it? I can't seem to find concordant alignment rates in a lot of the RNASeq literature, so I'm not sure if this is something a reviewer would wonder about.