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Fig. 2 | BMC Genomics

Fig. 2

From: Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds

Fig. 2

RNA-Seq analysis pipeline. Raw RNA-seq reads were checked for quality control (FastQC) and processed to remove adapters and low-quality bases (Trimmomatic, PrinSeq). Cleaned reads were either: mapped to the genome (GSNAP); or were used for de novo transcriptome assembly (Trinity) and mapped to the resulting transcriptome (GSNAP). Transcriptome-mapped and genome-mapped reads were compared at each stage of analysis: After mapping; after differentially expressed gene (DEG) identification (EdgeR, DESeq2, NoiSEQ), and after gene-ontology (GO) analysis (Blast2GO)

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