Identifying differential gene expression in RNA-seq reads

First we will be going through the process of identifying differential gene expression in RNA-seq reads. Launch GenePattern in the GenomeSpace UI. When loaded we can select the “CuffDiff” module which will be used to identify differential gene expression between conditions. From the GenomeSpace directory, select the wild-type RNA-seq data as input for the first condition, “wild-type”. Next, select the knockout RNA-seq data as input for the second condition, “knock-out”. We will input the mouse reference genome in the GTF file format. Next, ensure that you have selected the correct library type, “fr-unstranded”. In Advanced Parameters, input the minimum alignment count to be 0. Next, run your analysis. Next we will export the output from GenePattern’s “CuffDiff” module to GenomeSpace. To obtain the differential gene expression output navigate to the “Jobs” tab. and select the file “gene_exp.diff”. Select “Save to GenomeSpace” and select the folder you’d like to send this file to.

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