Table 1 Mapping percentages for the different RNA-seq methods and samples
From: mRNA-seq whole transcriptome profiling of fresh frozen versus archived fixed tissues
mRNA-seq | RiboZero | Nugen | |||||
|---|---|---|---|---|---|---|---|
FF | FFPE | FFPE old | FF | FFPE | FF | FFPE | |
n = 6 | n = 5 | n = 3 | n = 3 | n = 3 | n = 3 | n = 6 | |
Exons | 58 (51–63) | 29.2 (16.6–38.8) | 20.1 (13.8–32.2) | 21.4 (14.9–30) | 8.4 (0.6–12.7) | 20.3 (16–22.7) | 3.9 (0.8–7) |
Intronic/intergenic | 25 (20–32) | 28.2 (22.3–32.6) | 23.3 (18.9–27.4) | 44.4 (35.1–55.5) | 70.2 (61.7–75.2) | 65.1 (63.1–67.9) | 32.5 (24.5–43.1) |
rRNA | 1.3 (0.9–1.6) | 12.7 (4.17–17.8) | 6.4 (2.7–12.9) | 24.7 (1.15–45.3) | 5.3 (0.9–13.4) | 0.07 (0.05–0.08) | 1.2 (0.3–2.2) |
Multiple alignment | 11.9 (9.5–15) | 5.9 (3.8–7.2) | 4.2 (2.63–6) | 6.3 (2–10) | 6.5 (6.2–6.6) | 9.6 (8.7–10.3) | 3.6 (2.7–4.7) |
Unmapped | 3.8 (3.7–4) | 24 (10.9–44.9) | 45.7 (31.6–54) | 3 (2.7–3.3) | 9.6 (5.3–17.8) | 4.8 (4.2–6.1) | 58.7 (43–67.8) |