Hello, I'm currently working on RNA seq analysis of bacteria, and I found my data is contaminated by genomic DNA (although I use DNAseI). I've tried using SeqMonk, but the result hasn't improved. Can anyone recommend another tool I could use for this purpose? I have a single-end result using rRNA depletion (which did not work well and I had to use Sortmerna to clean up the reads).
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yahav.bracha •
Have you considered using a duplex-specific nuclease to remove the gDNA as it is dsDNA? The DSN would only remove the dsDNA (gDNA) and leave any ssDNA and RNA alone. Zymo Research has highly selective version of the DSN (PureRec Duplex-specific nuclease (DSN) that should help remove the gDNA contamination and allow you to get better RNA seq results.
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Based on random alignments across the genome outside of known exons? If not what are you basing that conclusion on?
You may want to try this package out: https://bioconductor.org/packages/release/bioc/vignettes/gDNAx/inst/doc/gDNAx.html