Is it possible for genomic DNA to be sequenced in a modern RNA-seq protocol?

Question

[predeus]

Hi all,

perhaps a very broad question more fitted to a different platform, but I was curious if someone had anything to say about this. How possible is it (depending on the RNA-seq protocol, but even in general) to sequence genomic DNA in RNA-seq? If someone has some interesting papers or discussions on the matter, I would be very grateful.

As always, thank you in advance!

-- Alex

Answer 1

[GenoMax]

Yes this question is more suitable for an experimental forum but that said it is possible to have gDNA contamination. It should be observable in a genome viewer like IGV as scattered read alignments (outside of gene models).

See: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08785-1

There are R packages to detect/address this:

https://www.mdpi.com/2673-6284/13/3/30
https://bioconductor.org/packages/devel/bioc/vignettes/gDNAx/inst/doc/gDNAx.html