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Table 2 Simulated datasets and their corresponding analyses in this study

From: Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets

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