Trimmomatic is a java tool for cut and filter reads

Capt to merger transcripts

Capt to merger transcripts

Samtools

Transcriptomic analysis of juvenile Chinese sea bass (Lateolabrax maculatus) anesthetized by MS-222 (tricaine methanesulfonate) and eugenol

Physiological and transcriptomic responses to fishmeal-based diet and rapeseed meal-based diet in two strains of gibel carp (Carassius gibelio)

Transcriptomic analysis of juvenile Chinese sea bass (Lateolabrax maculatus) anesthetized by MS-222 (tricaine methanesulfonate) and eugenol

Transcriptomic response to soybean meal-based diets as the frst formulated feed in juvenile yellow perch (Perca favescens)

Codes for hot to running EdgeR to call differential Expression Genes from RSEM result. (More details you can find in Trinity wiki)