We have RNA-Seq sequences in bam format and would like to perform gene expression analysis for specific genes. The most important step for us is to prepare count matrices.
- Is Bioconductor’s rnaseqGene the best tool to use for gene expression with RNA-Seq sequences? It appears to encompass all steps?
- Is gene expression analysis for RNA-seq data with DESeq2 a better tool to just obtain counts?
- After the gene expression analysis is complete, which tools are best to perform survival analysis using the counts ?