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.

1. Read processing and mapping.
2. Assembly quality control by use of Blobtools.
3. Filtering non-expressed genes
4. Differential Expression (DE) analysis via limma-VOOM

• Trimmomatic Publication | Manual
• FastQC Website
• HISAT2 Publication
• Samtools Publication | Manual
• cuffnorm Publication
• HTseq Manual
• Limma-VOOM Publication