3′ intervals | Nucleotide-conversion rate [%] | Read length [bp] | Coverage | Labeled transcripts | Analysis | Figure |
---|---|---|---|---|---|---|
1 k mESC expressed 3′ intervals of 1000 randomly selected transcripts expressed in mESC) | 0, 2.4, 7, 15, 30, 60 | 50, 100, 150 | 100 | 100% | Nucleotide-conversion aware read mapping | 2a,c, S1 |
1 k mESC expressed | 0, 2.4, 7 | 50, 100, 150 | 100 | 100% | Multimapper recovery strategy evaluation | 3b |
22,281 (mESC) | 0, 2.4, 7 | 100 | 60x | 100% | SNP masking evaluation | 4b |
1 k mESC expressed | 2.4, 7 | 50, 100, 150 | 100x | 50% | Evaluation of T > C read sensitivity / specificity | 5a, S4 |
18 example genes (mESC) | 2.4, 7 | 50, 100, 150 | 200x | 50% | Comparison of labeled fraction of transcript estimation methods | 5c |
1 k mESC expressed | 2.4, 7 | 50, 100, 150 | 25x- 200x in 25x intervals | 0–100% | Evaluation of labeled fraction of transcript estimation | 5d, S6 |