RNA-seq_analysis tools is a package of Python scripts designed primarily to analyse differential expression and splicing between samples using RNA-seq data. There are also scripts for obtaining gene/transcript sequences and co-ordinates. The scripts work on the output of the Tuxedo suite of tools for RNA-seq analysis (Trapnell et al., 2012) to identify genes, transcripts, or introns in spliceforms that are expressed above a user-specified threshold in one or more user-specified samples and at or below a user-specified threshold in one or more other user-specified samples.
To cite RNA-seq_analysis tools, please cite the following paper: Sutton ER, Yu Y, Shimeld SM, White-Cooper H, Alphey L: Identification of genes for engineering the male germline of Aedes aegypti and Ceratitis capitata. BMC Genomics 2016 17:948.
All the scripts in RNA-seq_analysis_tools require Python. They have been tested only with Python 2.7.3. Some of the scripts have further requirements; see the individual README files for more information.