Hello all! I was just wondering what the best method might be to use Salmon to map reads for both ribosome profiling and RNA-Seq and analyze the results using DESeq2. I have built a transcriptome with UTRs and used Salmon to map my reads. However, I want to only count reads that map to the CDS and not UTRs in the ribosome profiling dataset. Generating two different transcriptome indexes leads to problems with downstream analysis with DESeq2. For the profiling reads, would it be advisable to map against the transcriptome using an aligner such as Hisat2/STAR, manipulate the bam files to remove reads that align to UTRs, then quantify using Salmon? Would this lead to inaccurate quantification? If not, is there some way to use DESeq2 to analyze featureCounts quantified ribosome profiling reads against Salmon mapped RNA-Seq reads?