Bioinformatic analyses often require lengthy workflows or pipleines, where the output of program A feeds into program B, and so on. These programs may also not output their results in a format which is convenient to use in the subsequent steps, requiring writing a conversion script, or piping its output …

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When analyzing RNAseq you're faced with many possible analysis pipelines. The biggest decision you need to make is what the purpose of your experiment is. I will make the assumption that most of the time people want to determine which genes are differentially expressed between two samples, genotypes, conditions, etc …

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