Fig. 4
From: Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential
CfPeak is capable of identifying cfRNA peaks in novel transcripts. A Peak number distribution across known transcripts from 11 RNA species and novel transcripts from four regions. Peaks in repeats regions were shown in detail. B First column: Venn plot showed the number of intron-derived novel miRNA candidates newly identified by miRDeep2 and detected by cfPeak. Stem-loop RNA structure plot showed an example of novel miRNA candidate. Second column: pie plot showed the number of novel snoRNA candidates of two types identified by snoscan and snoGPS. Stem-loop RNA structure plot showed an example of novel C/D box snoRNA candidate. Third column: pie plot showed the number of novel tRNA candidates of two types identified by tRNAscan-SE. Stem-loop RNA structure plot showed an example of standard tRNA candidate. Fourth column: pie plot showed number of novel ktRNA candidates of two types identified by kturnSeeker. Stem-loop RNA structure plot showed an example of forward ktRNA candidate. Parts of peak regions detected in cfRNA sample (GSE71008 pool) were filled with red color in stem-loop RNA structure plot. C Coverage of extended regions in different cfRNA-seq datasets and several UCSC tracks near four candidates mentioned above. Y axis: min–max scaled depth. X axis: hg38 genomic coordinate. TGIRT, thermostable group II intron reverse transcriptases sequencing library; N4, optimized small RNA library (four degenerate nucleotides at the ligation ends); RGS, RNA G4 structural sites; RSS, RNA secondary structure