¿Could doubling the carrier RNA input during manual extraction using the QIAamp Viral RNA Mini Kit lead to increased non-target sequences in metatranscriptomic sequencing of microbial communities? I am using several types of samples like swabs, stool, serum and whole blood.
Povilas Kavaliauskas
Beatriz de Arco
Yes, absolutely it can. Qiagen kits usually use a polyA carrier and this will give you non-specific reads, depending on your approach. If you don't use DNase digestion and RNase suggestions for cDNA, this will increase the rubbish reads.
In this case, especially in low abundance samples such as sera, your carrier RNA might dominate your reads.
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