In short: I developed a program as a GUI to help set up and execute RNA-Sequencing analysis via Kallisto and DESeq2, starting with fastq files, either downloaded with directions from the program, or provided by the user. The program provides customized Bash and R scripts to automate the process (based on your own file structure), providing output including transcript level abundances, a normalized counts matrix, a list of up- and down-regulated genes, hierarchical clustering heatmaps, PCA plots, and bi-modality analysis via the SIBER and DEXUS packages. Check out my Github repo and follow instructions on the ReadMe. Please see an example of the pipeline output here.
And for a little more background...
Without knowledge of the Bash and R programming languages, it can be confusing to newcomers how to set up the proper file structure and how to execute the proper commands that are necessary for using Bioinformatics packages such as Kallisto and DESeq2.
I set out to help those that are new to the RNA-Sequencing world by creating an application to automate the process of file structure creation and command execution that are necessary for downloading fastq files via the SRA toolkit, sequence alignment via Kallisto, and differential expression analysis via DESeq2. The user only needs a path to their working directory, the sample names (and NCBI accession numbers if downloading fastq files), and whether the reads are paired or single end. The user is provided with a set of detailed instructions and customized code snippets that allow for easy execution of required commands in both Bash and R. In the end, a pipeline for RNA-Sequencing analysis is provided to produce the output described above.
To begin, visit https://github.com/anthony-knox/rna-sequencing-pipeline-generator and proceed with the directions in the ReadMe. If you have any questions, don't hesitate to ask in this thread or by contacting me via my Github profile.
UCSF, Department of Pathology