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Fig. 3 | Genome Biology

Fig. 3

From: The impact of read length on quantification of differentially expressed genes and splice junction detection

Fig. 3

Comparison of previously reported qPCR results with our DEG results. a Pearson correlation between Log2FC of genes according to various differential expression methods and qPCR. Single-end 25 bp reads have the worst correlation when using DESeq and EdgeR. b Root mean square deviation (RMSD) between Log2FC and qPCR. Single-end 25 bp reads give results farthest from the true values. c Common genes between the top 200 genes identified by various differential expression methods and qPCR sorted by +Log2FC. d Same as (c), except sorted by –Log2FC. The overlap of common genes improves as read length increases. However, the gain is not significant for reads >50 bp for paired-end and >75 bp for single-end reads

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