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
1 answer
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
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