Transcript Quantifier Assessment

Assessing StringTie, Salmon, and Kallisto with simulated RNA-Seq reads with noises introduced in read- and annotation-level.

Data

We used the simulated data from the transcriptional noise work of Varabyou et al [1]. In total, there are three tissues, and each of them has 10 samples. Three different transcriptional noises are simulated which are (1) intronic, (2) intergenic, and (3) splicing noises.

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Experiment Design

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Teamwork

Kuan-Hao Chao	Peter Ge
1. Experiment design	1. Result visualization
2. Running StringTie, kallisto, and salmon	Github Maintaining
3. Github Maintaining

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Reference

1. Varabyou, A., Salzberg, S. L., & Pertea, M. (2021). Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments. Genome research, 31(2), 301-308.