I have some RNA-Seq data with a low proportion of reads aligning to the human genome (<50% in most samples, <20% in one or two). The sample prep involved very low numbers of human cells and so we are wondering if bacterial or fungal contamination could have occurred which may explain this.
Does anyone know of a resource/technique whereby I could test for this contamination? At the moment I am downloading bacterial 16S ribosomal sequences from RDP to see if I can align reads to those, but I'm wondering if there isn't a better way.
Does anyone know of a resource/technique whereby I could test for this contamination? At the moment I am downloading bacterial 16S ribosomal sequences from RDP to see if I can align reads to those, but I'm wondering if there isn't a better way.
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