Removing gDNA contamination from RNA seq data

Question

[yahav.bracha]

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).

[GenoMax]

I found my data is contaminated by genomic DNA (although I use DNAseI)

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