Hello to everyone.
In my group, we are using RNA-Seq to study the expression of bacteria under different conditions, isolated or as dual-transcriptome when in association with plants.
When checking the table of total counts for each gene, I can observe an important number of reads mapping against the rrna genes, mostly 16S and 23S. I also found a similar amount of read counts mapping against rrnas when analyzing a dual experiment where no bacteria was present, just plant material.
Illumina reads from HiSeq200 were treated by TopHat and Cufflinks. Library preparations followed a RiboZero Gold treatment + TruSeq Stranded Total RNA kit. Additionally, rrna depletion was verified by running Bioanalyzer.
Have any one an idea where this mapping might come?
Thanks in advance for your help.