Is there a difference between RNAseq and CAGE data analysis?

[Fernas]

I have N fastq files for some samples. some were generated using RNA-Seq technology and some other were generated by sequencing CAGE libraries.

I am about to start processing all these files (quality control, trimming, adapter removing, alignment, read count extraction, normalization, differential gene expression...etc).

My question is:
Is there any difference between processing RNASeq fastq files and CAGE fastq files?

[Dario1984]

They are different assays for different purposes. The reads of CAGE-seq are much shorter than RNA-seq. CAGE-seq reads almost always begin with G because of the experimental protocol. This adds a mismatch to the reference sequence, unless it also contains G one position before the start of the read. For RNA-seq you want to count all of the reads in exons, whereas for CAGE-seq you want to select peaks and count just within the peaks. You mustn't use the same analysis for both of them.