In this repository, I summarize the scripts and tools I used to perform the transcriptomic analysis of Sclerotinia sclerotiorum and Sclerotinia trifoliorum. Plotting scripts are included as well. The publication can be found here.
- Read processing and mapping.
- Assembly quality control by use of
Blobtools. - Filtering non-expressed genes
- Differential Expression (DE) analysis via
limma-VOOM
- Trimmomatic Publication | Manual
- FastQC Website
- HISAT2 Publication
- Samtools Publication | Manual
- cuffnorm Publication
- HTseq Manual
- Limma-VOOM Publication