Computational protocol: Genome-Wide Epigenetic Regulation of Gene Transcription in Maize Seeds

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Protocol publication

[…] RNA-seq datasets were aligned to the maize reference genome using tophat []. The resulting alignment files were subjected to Cufflinks [] to generate a transcriptome assembly and make the annotation. Reads per kilobase of transcript per million reads (RPKM) were calculated. Five ranges of RPKM values representing different expression levels were collected and associated with DNA methylation and sRNA accumulation. […]

Pipeline specifications

Software tools TopHat, Cufflinks
Application RNA-seq analysis
Organisms Zea mays, Arabidopsis thaliana, Homo sapiens