I'm new to RNAseq and have a couple of questions I would love to get some help with. I want to preform RNAseq on small cell numbers of mouse and human cells and am considering using the Nugen Ovation kit. There doesn't seem to be much published data using this kit, but per the posters on their website (e.g. http://www.nugeninc.com/tasks/sites/...Seq_poster.pdf) they show that ~50% of total reads map uniquely, and ~15% of total reads map to RefSeq. A recent Biotechniques paper (http://www.ncbi.nlm.nih.gov/pubmed?term=21486238) using the kit indicates ~25% map to RefSeq . I have two questions:
1) Is 15%-25% of RNAseq reads mapping to RefSeq what one would see using the standard Illumina procedure starting with mRNA? It seems surpisingly low.
2) How many mapped reads are generally needed to get robust expression measurements? Specifically, how many mapped RefSeq (or equivalent) reads do people feel give sensitivity comparable to microarrays.
1) Is 15%-25% of RNAseq reads mapping to RefSeq what one would see using the standard Illumina procedure starting with mRNA? It seems surpisingly low.
2) How many mapped reads are generally needed to get robust expression measurements? Specifically, how many mapped RefSeq (or equivalent) reads do people feel give sensitivity comparable to microarrays.
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