Fig. 2

Local and global reproducibility in RP replicates. The figure presents the inter-replicate variance for a measured nucleotide position in the transcript (blue) and for complete genes (red). Y-axis is the standard deviation of the fraction of total read counts (RCs) measured in replicate 1 (read count 1, RC1), while the X-axis denotes the total number of read counts in that position in both replicates (RC1, RC2). Each point (bin) is based on the standard deviation of 1000 positions in the dataset for nt-reads, or 100 positions for gene-reads. The confidence in the measurement increases (the variance decreases) with the total read count, as expected. The difference between the two profiles indicates that additional noise and bias exist at the nucleotide level, that is considerably higher than in the gene level. This noise/difference is evident even after the profiles reach plateau, and its gain varies from experiment to experiment. Repeated for: a Ingolia-2009 [10]; b Li-2012 [36]; c Stadler-2011 [26]; d Ingolia-2011 [38]