I have 2 sets of fastq files from another collaborator. The first is contains exome data and the second contains RNAseq data. But both have the RNA in the name but a different ID. How do I differentiate between a fastq file between exome seq and RNAseq?
Absolutely agree with James that you should ask your collaborators, but purely as an academic exercise... assuming you have a good reference genome+annotation (e.g. human/mouse), whole exome seq should align to mostly annotated exonic, RNA-seq to exonic+intronic, and whole genome seq to exonic+intronic+intergenic sequences. Sequence duplication levels may also be higher for RNA-Seq with highly expressed genes often 'deeply' sequenced