Fig. 1

Ub-ISAP pipeline schematic diagram. Candidate reads having the TR-based primers are selected and primers were trimmed off both the 5′ and 3′ prime ends of selected reads. These reads are aligned against the reference host genome using Bowtie2 allowing no mismatches. The paired-end reads that align concordantly only at one location are selected for annotation, whereas single end reads that align only at one location are realigned twice allowing one and two mismatches respectively. The reads that align only at a single position after final alignment are selected for annotation. The unique reads are classified as TSS-proximal, intragenic and intergenic