Fig. 1

Schematic representation of RCRUNCH. a Overview of the workflow. b Scatterplot of the proportion of reads (log₂) in individual genomic regions in a foreground (IP) sample generated by eCLIP for the PUM2 protein (replicate 2 of dataset ENCSR661ICQ from the ENCODE project, see “Methods”) and a corresponding background sample (SMI). Each dot corresponds to a 300-nucleotide-long genomic region. Marked in color are regions that are enriched in reads in the foreground relative to the background sample (FDR < 0.1, see color legend). Three genomic regions (zoom-ins in c) with various enrichment scores are marked with stars. c Coverage of three overlapping genomic regions (highlighted in b and indicated at the top of the panel) by reads from the IP (light gray) and SMI (yellow) samples (RPM—reads per million). The significant peaks identified in the genomic region spanned by the three windows are shown in red. The blue line shows the number of read starts (5’ end of mate 2 reads) from the IP sample in the genomic region. Read starts indicate crosslinked nucleotides, where the reverse transcriptase falls off during sample preparation