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Fig. 5 | BMC Genomics

Fig. 5

From: Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction

Fig. 5

Effect of rRNA Depletion Chemistry on Spike-In Controls: a) Effect of degradation of SIRVs on the ratio of SIRV reads to ERCC reads in each replicate. Percent of reads mapping to SIRVs out of total reads mapping to Spike-ins in shown. Data sets ordered by intact/degraded status followed by site within each kit left to right. b) Relative ratio of reads mapping to SIRV1. Fraction of reads mapping to each isoform of SIRV1 are shown for each replicate. Expected fractions shown as dark horizontal lines. Light horizontal lines show 2-fold changes in fraction observed (log scale). Each SIRV1 isoform is shown in a different color. Replicates ordered as in a. c) Boxplot of normalized transcripts per million (TPM) for subsets of SIRVs. SIRVs present at 4×, 1× and 1/4× in the pool were randomized and normalized TPM scores for all sites for two sets of 10 SIRVs were plotted across different chemistries using intact samples. 5th, 25th,Median, 75th and 95th percentile are shown. d) Boxplot as in c except red boxplot highlights shortest quintile (len < 480 nt) and green includes longest quintile (len > 2200). e) Boxplot as in c except red boxplot highlights lowest GC quintile (< 36% GC) and green includes highest quintile (> 44.5% GC). f) Boxplot as in c except red highlights random set of 10 transcripts included at 4× while green includes set of 10 transcripts at 1/4×

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