Hi folks, I just have a quick question which hopefully has a simple answer. I downloaded from NCBI a set of fastq files containing mouse RNA-seq data which was generated using "classic" TruSeq RNA-library preparation kit. Hence it contains reads from the whole mRNA molecule. I want to align (and then count) reads that do map only the 3' UTR region. I am currently using STAR to map the reads and the star index was built with the latest Ensembl .gtf and .fasta files.
Any suggestion will be much appreciated Thanks Luca