I have just started collaboration on a ribosome profiling project. We have ~30bp illumina single end reads (adaptor removed). These sorts of data are new to me and I am looking for some advice on prudent and well established analyses.
Here are my questions:
What are people using to align short RNA sequences?
I was thinking Bowtie 2 or BWA.
Should I toss out tRNAs and rRNAs prior to the alignment step?
One PI said yes, but I am not convinced. The tRNA and rRNA are in the reference genome and I figured I could mask them out later.
What bioinformatic controls are there?
I was going to look at some house keeping genes, but don't know of a metric to use.
Besides my experiment specific questions, what analyses are commonplace?
Any must read papers?