Please see the TopHat_Workflow, Splicing_Workflow, and Mutation_Workflow for specific acknowledgements.
I apologize for the confusion, but I would like to emphasize that these are called “templates” because I almost always have to modify the code for each project (beyond the parameter files), meaning they will be more difficult for other people to use in the same way. This was unfortunately not immediately clear to me when I created the templates.
I also believe that the process of writing the scripts for analysis (such as the templates) is very important for the learning process, and it is very important that you understand all the steps for analysis before presenting them in a paper.
So, I will post an update when more specific guidance / suggestions can be provided. In the meantime, I apologize, but I cannot provide user support for the templates.
template scripts for RNA-Seq analysis
Genome_Ref_Code is used to prepare annotations for TopHat_Workflow
Transcriptome_Ref_Code is used to prepare sequences / annotations for Transcriptome_Workflow
Splicing_Workflow and Mutation_Workflow use genomic alignments
Splicing_Workflow uses TopHat alignment from TopHat_Workflow, but provides new quantification for exons / splice junctions
Mutation_Workflow uses 2-pass STAR alignment for GATK variant calling
Please see the README file in each section.