Fig. 1

Schematic of the ROP. Human reads are identified by mapping all reads onto the reference sequences using a standard high-throughput mapping algorithm. ROP protocol categorizes mapped reads into categories of genomic (red colors) and repetitive (green colors) reads. Unmapped reads that fail to map are extracted and further filtered to exclude low-quality reads, low-complexity reads, and reads from ribosomal DNA (rDNA) (grey color). ROP protocol is able to identify unmapped reads aligned to human references with use of a more sensitive alignment tool (lost human reads: red color), unmapped reads aligned to human references with excessive (“hyper”) editing (hyper-edited RNAs: cyan color), unmapped reads aligned to the repeat sequences (lost repeat elements: green color), unmapped reads spanning sequences from distant loci (non-co-linear: orange color), unmapped reads spanning antigen receptor gene rearrangement in the variable domain (V(D)J recombination of B cell receptor and T cell receptor: violet color), and unmapped reads aligned to the microbial reference genomes and marker genes (microbial reads: blue color)