The protocol paper for tophat/cufflinks is quite good:

http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html

It covers an RNAseq differential expression workflow. I think you may be looking for something at a more detailed level of complexity (i.e. what exact commands are run) in which case you will be better of looking at some R vignettes or tutorials. Research papers are usually biology focused (where as the workflow is not as important as the results, and therefore not covered in depth) or software focused (where as the go into intricate detail about the workings of one piece of software)

Here are some links to tutorials:

• https://www.broadinstitute.org/gatk/guide/topic?name=tutorials
• http://www.bioconductor.org/help/workflows/rnaseqGene/
• http://quinlanlab.org/tutorials/bedtools/bedtools.html
• https://wikis.utexas.edu/display/bioiteam/Variant+calling+using+SAMtools

I will note that some of these tutorials are written for people working on workshops or in set up environments so you may have to do some fudging to get stuff working with your own sample data.