[Under development] Comprehensive Nextflow-based pipeline for RNA-seq analysis of cancer samples.
Tools:
- QC with FastQC
- Read alignment with STAR
- Gene expression quantifiaction with HTseq
- Cancer type prediction using kNN and The Cancer Genome Atlas as a reference
- Alignment post processing for variant calling with GATK4
- Variant annotation with VEP
- Conversion of annotated variants from VCF to MAF format
- Isoform-level gene expression quantification with Kallisto
- RNA-based fusion gene prediction with Pizzly