Experimentally measured background reads distinguish commonly detected background sites from authentic binding events. Three representative examples of genomic regions containing PAR-CLIP reads: MATLAT1 lncRNA, ELAVL1 coding sequence (CDS), and ELAVL1 3’UTR. MALAT1 lncRNA and the ELAVL1 CDS have significant background binding (three middle panels G20, G35, G45) while the definitive HuR RBP binding site in ELAVL1 3’UTR lacks any reads from background libraries but contains reads in the total (Tot) library. Grey bars represent unique sequencing reads while blue/red marks or green/tan marks represent T-to-C conversions detected on the positive or negative genomic strand, respectively. The numbers in the upper left corners are the scale of the maximum read depth for an individual nucleotide. Depictions of these binding events to the full-length MALAT1 and ELAVL1 transcripts are shown in Additional file 3: Figure S3 and Additional file 4: Figure S4, respectively.
Friedersdorf and Keene Genome Biology 2014 15:R2 doi:10.1186/gb-2014-15-1-r2