How to choose the optimal RNA-Seq library characteristics for alternative splicing analysis (with MAJIQ)

---

This Github repository provides the code the for the publication Ladwig et al. 2024.

Authors

• Annika Ladwig
• Melina Klostermann
• Kathi Zarnack

1 Preprocessing and alternative splicing analysis with MAJIQ

---

The Rmarkdown contains the code for the preprocessing of the raw reads and for the subsequent alternative splice analysis with MAJIQ.

The rendered HTML file is available at https://annikala.github.io/.

2 Impact of library characteristics on alternative splice analysis

---

The R scripts contain the code used to investigate the influence of read length (2.1a - U2AF2 KD, 2.1b - UPF1 KD), read depth (2.2) and replicate number (2.3) on:

• read alignment
• LSV detection
• LSV quantification
• alternative splicing event types distribution

3 Impact of library characteristics on the detection of local splice variations (LSVs) in lowly expressed genes

---

The R script '3_TPM_analysis.Rmd' contains the code for analysing the impact of read length and read depth on the detection of LSVs in lowly expressed genes.