You've got data. We turn it into information
This is how I do some of the standard analyses. I am constantly evaluating and changing my procedures, so this may be out of date. You will want to change file names, directory structure, and such. If running on the HPC, you'll need to wrap the commands in a script to submit. You may (will) have to load modules, and some of the commands may be (are) slightly different on different machines.
Filter from sam file
Online tool here. Before using, make sure your mapper sets the flags you are interested in.
Prepare UCSC gtf file for useThe UCSC gtf files have bad names. They need to be changed. Do this by also downloading the kgXref file, edit so that it is just UCSC,Name
For questions, help, or to offer a beer, get in touch with the bioinformatician, Niel Infante