Effects of uniqueness normalization on expression level.
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(A) Histogram showing how uniqueness compensation using MULTo affects the RPKM values at different read lengths. The x-axis show the difference in gene expression between uniqueness compensated and uncompensated expression levels. (B) RPKM values for FTH1 before and after uniqueness normalization. (C) Read coverage and uniqueness profile across FTH1 for 25 nt reads. Uniqueness density was calculated as the proportion unique reads aligning to each genomic coordinate.