My PhD project involves fusion gene detection from cancer data of TCGA and ICGC portals. I find that the RNAseq files (fastq,bam formats) are mainly closed access, whereas the clinical or expression data (In CSV OR TSV format mainly) are freely available. Most of the publications related to this use the fastq/bam data. My question is, is it possible to detect gene fusions using command line tools (STARFusion, GFusion, JAFFA for example) using those freely available clinical data ? Are there any publications using these data available?
I am kinda new to this, so any input will be appreciated.