RNA-seq and whole exome sequencing
We have analyzed data from matched tumor/normal samples from two uveal melanomas patients with easy-to-use workflows implemented in CLC Cancer Research Workbench to investigate the benefits of RNA-seq compared to whole exome sequencing.
For data analysis, CLC Cancer Research Workbench provides ready-to-use workflows combining tools like read mapping, annotation, and reporting.
For variant calling, we use the “Identify Variants” workflow and tumor-specific variants are identified using the “Filter Germline Variants from Tumor Normal Pair” workflow.
Following variant calling and filtering, variants from the whole exome sequencing and the RNA-seq data are compared.
- CLC Cancer Research Workbench provides easy-to-use workflows that include algorithms for read mapping, variant calling, filtering, and annotation.
- The tool “Identify Known Mutations from Sample Mappings” provides a more reliable method compared with variant calling to recover variants previously detected in WES data.
- The analysis of whole exome sequencing and RNA-seq data sets can easily be combined using the tools provided in CLC Cancer Research Workbench .
- In comparison to WES, RNA-seq reports only those candidate variants being expressed.
Get more information about comparison of variant calling from whole exome and transcriptome sequencing data using CLC Cancer Research Workbench:Application note