Nt1310 Unit 2 Case Study

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Figure 5.7. illustrates that the length of the DNA fragments in both runs was between 10 and 20 kb. In the first line, The Thermo Scientific GeneRuler 1 kb Plus DNA Ladder (Thermo Fisher Scientific, Waltham, USA) was applied. In the second line, the sample was added. The ladder is composed of 15 individual DNA fragments of 20000 bp, 10000 bp, 7000 bp, 5000 bp, 4000 bp, 3000 bp, 2000 bp, 1500 bp, 1000 bp, 700 bp, 500 bp, 400 bp, 300 bp, 200 bp and 75 bp. In each run, the DNA fragments in the sample presented a band between 10000 and 20000 bp.
The characteristics of the two different runs can be found in Table 5.1.. In run 2 more DNA fragments were obtained, the total DNA yield was higher and the longest fragment was 441583 base pairs longer than the longest fragment in run 1. …show more content…
(run 2) the 2D sequence length versus the quality score is visualized. Comparison of the sequence length of run 1 and 2 shows that the three changes that were made in order to have less short fragments were efficient, even though the mean read length is lower in the second run. The quality score is an arbitrary parameter, which helps to assess the quality of the data. When the quality score is more than nine, the data have a good quality. A quality score between eight and nine is acceptable. If the quality score is below eight, the quality of the data is too bad to be useful. The quality of the reads is significantly higher in the second run. Next to the different library preparations, the lower quality of the first can be due to the use of fuel mix from different production lots. The fuel mix used in the first run originated from a lot with production
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