poojasingh09/2024_singh_transcriptomeanalysis_pipeline: Transcriptomics pipeline for accurate gene and isoform analysis

This is a set of scripts used to analyse short-read illuminated transcriptome data from hundreds of mRNAseq samples across multiple species and radiations for cichlid fishes from the East African Great lakes. The analysis leverages short-read mRNA-seq to assemble a super-annotation of gene isoforms that can be used to conduct differential splicing analysis at the isoform level. The manuscripts that used this pipeline are as follows: Singh et al 2025 parallel lakes analysis (in submisison); Duenser, Singh et al 2025 lake victoria ontogenetic analysis (in review ProcB); Singh et al red-yellow carotenoid based coloration (in revision MolEcol) Singh et al in prep meta-analysis of all available transcriptomes; If you use this code please cite Singh et al 2025 parallel lakes paper (in submisison). If you have questions, email pooja.singh09@gmail.com with the email header: your RNAseq pipeline.