Fig. 4.

Partial automation of the curation process. a Number of L1 loci with mapped reads upstream by 1000 bps in the same orientation from replicate 1, strand-specific, whole-cell RNA. b Number of loci with mapped reads upstream by 5000 bps in the same orientation from replicate 1, strand-specific, whole-cell RNA. The total 285 L1 loci identified to have uniquely mapped reads in the sense orientation to full-length L1 s in the human reference genome in replicate 1, whole-cell RNA-Seq data of 22Rv1 were separated by loci curated to be consistent with expression from the L1 promoter (true) and loci falsely expressed from a different promoter and then compared to regions of upstream, sense expression in a proportional Venn diagram [31]. In light green are the L1 loci identified to be authentically expressed after manual curation in which there were zero mapped reads upstream in the same direction for up to 1 or 5 kb upstream. In dark green are the L1 loci identified to be authentically expressed after manual curation in which there were a few mapped reads upstream in the same direction for up to 1 or 5 kb upstream. In light red are the L1 loci identified to have expression unrelated to L1 promoter transcription after manual curation in which there were mapped reads upstream in the same direction for up to 1 or 5 kb upstream. In dark red are the L1 loci identified to have expression unrelated to L1 promoter transcription after manual curation in which there were not mapped reads upstream in the same direction for up to 1 or 5 kb upstream. The numbers of L1 loci in each group are denoted within the Venn diagrams