I have Illumina 100 bp paired end RNA-Seq data from a non-model species. I mapped it to the closely related genome available and I used STAR to do this task. I mainly did this to see if I could use the genome of the organism for a genome guided assembly. It turns out that I got an overall alignment rate of 0.93%. I used default parameters for this, however working around the parameters only increased the results to 1-2%. The species I'm working with is a cephalopod.
I'm not really interested in increasing the mapping rate at this point (since this was mainly for exploratory analysis). However I wanted to know what other downstream analysis can I do on the reads that actually did map (I'm assuming these would be tRNAs, histones etc). Basically I want to be able to make plots for the sequences that did align, but not sure what programs I can use to represent my data. Any ideas would be great :)
I also wanted to know if others have done a similar analysis and got similar results? What conclusions did you derive from this sort of analysis?