wwany / vasaseq_2022

This repository aims to serve as an index of the work described at Salmen & De Jonghe et. al 2022

Index for the computational methods used in the VASA-seq manuscript

This repository aims to serve as an index of the main computational methods implemented in the VASA-seq manuscript:"Droplet-based single-cell total RNA-seq reveals differential non-coding expression and splicing patterns during mouse development" (Salmen & De Jonghe et al. 2022). Some computational workflows were exclusively developed for this project and the corresponding code is contained in this repository. External workflows were also implemented and adapted for conducting part of the analyses and the respective code is distributed across separate repositories that are herein referenced.

The computational work carried out in this manuscript is divided into two main modules focused on (I) Gene expression and (II) Alternative splicing analyses. Each of these modules have several sub-sections, where corresponding material and descriptions are contained across the folders present in this repository.

• I. Gene expression
  • a. Mapping
  • b. Analysis
• II. Alternative splicing
  • a. Transcriptome assembly
  • b. Microexon annotation
  • c. Event-based quantification
  • d. Analysis

The manuscript is currently deposited on the biorxiv pre-print server, embedded in the following URL: https://doi.org/10.1101/2021.09.15.460240

The dataset can be accessed on Gene Expression Omnibus with the accession number: GSE176588