Table 2 Description of each quality metric color-rank scheme
From: SEAseq: a portable and cloud-based chromatin occupancy analysis suite
Quality metrics | Rank | ||||
|---|---|---|---|---|---|
Excellent | Good | Average | Below-average | Poor | |
Aligned percent (\(A\)) | \(A \ge 80\%\) | \(A \ge 70\%\) | \(A \ge 60\%\) | \(A \ge 50\%\) | \(A < 50\%\) |
Base quality (\(B\)) | B = “pass” | - | B = “warn” | - | B = “fail” |
Estimated fragment width | – | – | – | – | – |
Estimated tag length (E)a | \(E < \pm 10\) | – | – | – | \(E > \pm 10\) |
FRiP (\(F\))c | \(F \ge 0.05\) | \(F \ge 0.02\) | \(F \ge 0.01\) | \(F \ge 0.0075\) | \(F < 0.0075\) |
Linear stitched peaks (\(L\)) | \(L \ge 10000\) | \(L \ge 5000\) | \(L \ge 2000\) | \(L \ge 1000\) | \(L < 1000\) |
NRF | \(NRF \ge 0.8\) | \(NRF \ge 0.7\) | \(NRF \ge 0.6\) | \(NRF \ge 0.5\) | \(NRF < 0.5\) |
Normalized Peaks (N) | \(N \ge 10000\) | \(N \ge 5000\) | \(N \ge 2000\) | \(N \ge 1000\) | \(N < 1000\) |
NSCc | \(NSC \ge 1.045\) | – | – | – | \(NSC < 1.045\) |
Sequence diversity (\(D\)) | D = “pass” | – | D = “warn” | – | D = “fail” |
PBC (\(C\))c | \(C \ge 0.9\) | \(C \ge 0.75\) | \(C \ge 0.66\) | \(C \ge 0.5\) | \(C < 0.5\) |
Peaks (\(P\)) | \(P \ge 10000\) | \(P \ge 5000\) | \(P \ge 2000\) | \(P \ge 1000\) | \(P < 1000\) |
Raw reads (\(R\)) | \(R \ge 30 M\) | \(R \ge 25 M\) | \(R \ge 20 M\) | \(R \ge 15 M\) | \(R < 15 M\) |
Read length | – | – | – | – | – |
RSCc | \(RSC \ge 1\) | \(RSC \ge 0.75\) | – | – | \(RSC < 0.75\) |
Super stitched peaks (\(S\))b | \(S \ge 0.2\) | \(S \ge 0.1\) | \(S \ge 0.05\) | \(S \ge 0.02\) | \(S < 0.02\) |
Overall quality (Q) | \(Q \ge 2\) | \(Q \ge 1\) | \(Q \ge 0\) | \(Q \ge - 1\) | \(Q < - 1\) |