Tools to detect the bacterial sequences from mouse RNA-seq data

Question

[shome]

Is it possible to find out the bacterial sequences from host RNA-seq data ? Also,how to find the extent of bacterial expression in this data ?

[Thind amarinder]

There is the possibility to look for various bacterial contamination in the host RNA-Seq data, but to get an idea about the abundance of various bacterial species. Take a look on this paper and decontaminer tool