I typically work on the programming/data management side of things, but we're short-staffed and tricky analysis jobs sometimes work their way to me when others can't figure them out. In this case an investigator has human tissue that may contain bacterial contamination. He would like to determine whether this is true by extracting and sequencing the RNA from the sample, and then seeing if any of the reads are bacterial in origin. I don't know if this is preferable to other tests (like biochemical assays and whatnot), but I don't know enough to offer a better suggestion.
My first thought (as someone who doesn't do this kind of analysis regularly) is to do a standard alignment via bwa or tophat and store the unmapped reads in a file. Then these unmapped reads can be searched against a file or database to see if anything interesting pops up.
The tricky part here is that while it would be trivial to search against a single organism's genome, I don't know if a database of conserved bacterial sequences exists that I could search against. If such a thing exists then that's a possible solution.
Anyone have any ideas?