I map RNA-seq fastq files to the mouse genome (GRCm38) using the RNA-seq Analysis tool available in CLC Genomics workbench 9. As a result I get mapping results to ~46K genes. This is including non-coding genes. I would like to only map to protein-coding genes as I'm working with sequencing data of libraries that are prepared with Illumina TruSeq kit that captures mRNA by Oligodt beads.
Does anyone have experience with RNA-seq analysis in CLC Genomics? Is there a way of only mapping protein-coding genes in CLC Genomics