Fig. 5

Comparison of mapping features between live and fixed cells. (A) Mapping coverage of transcripts grouped by different lengths was used to show the variance in transcript mapping depth between live and fixed cells. Highlighted bars in the top-right corner shows the length of transcripts involved in that plot. Bias at 3’ end in fixed cells is more obvious for longer transcripts. (B) Difference in the mapping depth between groups. Ten groups of transcripts were separated by either GC-content (top) and length (bottom). The difference in depth is plotted against distance from 3’end to show how the variance changes. (C) The mapping ratios for each transcript were compared using coverage integrity correlation. Transcripts with top or bottom 10 % rank in length and GC content are highlighted in each correlation plot. (D) Visualization of the ratio of live/fixed mapping integrity showing transcripts with better coverage. Transcripts are sorted and grouped by length and GC content; each unit represents an average ratio for those transcripts. In the corner containing transcripts with longer and GC-rich transcripts, live cells are shown to have more complete mapping compared with fixed