We are seeing very large spikes in RNA seq reads in introns using the Nugen WT Ovation pico prep method. These peaks dominate the read profile even more than exonic reads. As a result reads mapping to "transcriptome" (ie cDNA) drops to below 30%. The peaks are very consistent between samples. Does anyone else see this and have an explanation for it or do we have a technical problem here?
I did wonder if its a result of the rather odd amplification method (polymerase run off) or perhaps "non-random" random priming?
I did wonder if its a result of the rather odd amplification method (polymerase run off) or perhaps "non-random" random priming?
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