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Fig. 2 | Genome Biology

Fig. 2

From: Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins

Fig. 2

Quantification of repetitive elements and other non-uniquely mapped reads. a Graphical representation of repetitive element mapping. Reads are mapped to human genome (requiring unique mapping) and a database of repetitive element families. Reads are then associated with RNA element families based on mismatch score, with (red) reads discarded if mapping equally well to more than one family. b Stacked bars indicate the number of reads from TROVE2 eCLIP in K562 that map either uniquely to one of four primary Y RNA transcripts, map uniquely to Y RNA pseudogenes (identified by RepeatMasker), or (for family-aware mapping) map to multiple Y RNA transcripts but not uniquely to the genome or to other repetitive element families. c Stacked bars indicate the fraction of reads (averaged between replicates) of all 223 eCLIP experiments, separated by whether they map (red) uniquely to the genome, (purple) uniquely to the genome but within a repetitive element identified by RepeatMasker, or (gray) to repetitive element families. Datasets are sorted by the fraction of unique genomic reads. d Heatmap indicates the relative information for 26 elements and 168 eCLIP datasets, requiring elements and datasets to have at least one entry meeting a 0.2 relative information cutoff (based on Additional file 3: Fig. S2d). See Table 1 for RBP:element enrichments meeting this criteria and Additional file 5 for all enrichments

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