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.
- Annika Ladwig
- Melina Klostermann
- Kathi Zarnack
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/.
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.