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The primary analysis is composed of the steps to go from the raw fastq files generated by the sequencing to the expression matrix containing the raw counts for each sample and for each gene.
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![overview](uploads/9855695405d57446ffa0b7dc659ce0d3/fastq.png "Overview of the primary analysis pipeline")
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![overview](../uploads/9855695405d57446ffa0b7dc659ce0d3/fastq.png "Overview of the primary analysis pipeline")
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## Demultipexing
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