Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols.

BMC Genomics · 2017 · PMC5442695 · PMID 28535780

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showed a trendno p-value reported

Whilst SE data showed a trend towards decreased read counts per gene, the NS data was more variable with read counts being higher for some genes but lower for others.

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