Hi Everyone,
I am working with single cell RNA-Seq and am currently analyzing my data. I've noticed that I often get a lot of reads aligning to the UTR but not at all to the exons. When I look closer, I see that there is often a poly A region here.
So, my question: Poly A tail selection using the Clontech SMARTer technology is supposed to only target mRNA (and lncRNA). However, is it possible it also sometimes catches genomic DNA? Or will the fact that it's double stranded prevent the Clontech adapters from binding to the region? Anybody else have problems with genomic contamination? Or perhaps you have another theory why I'm seeing a lot of specific alignment to to multiple areas with genomic polyA regions?
Thanks for your insight!
I am working with single cell RNA-Seq and am currently analyzing my data. I've noticed that I often get a lot of reads aligning to the UTR but not at all to the exons. When I look closer, I see that there is often a poly A region here.
So, my question: Poly A tail selection using the Clontech SMARTer technology is supposed to only target mRNA (and lncRNA). However, is it possible it also sometimes catches genomic DNA? Or will the fact that it's double stranded prevent the Clontech adapters from binding to the region? Anybody else have problems with genomic contamination? Or perhaps you have another theory why I'm seeing a lot of specific alignment to to multiple areas with genomic polyA regions?
Thanks for your insight!
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