Fig. 2.

Computational pipeline for the characterization and analysis of Olfr 3’UTR isoforms from RNA-Seq datasets. The pipeline is divided into six steps: Step 1: RNA-Seq reads are mapped using STAR, and reference genome and annotation files. Step 2: A mask file in bed format, restricted to the Olfr loci in mouse, is generated. Step 3: The mask genome alignment output is obtained. Step 4: Full known and novel transcripts are reconstructed with IsoSCM or Cufflinks. Step 5: Reconstructed transcripts are characterized and analyzed in terms of annotation, 3’UTR isoforms identification, identification of predictive PASs at 3′ ends, merging (merge of 3’UTR isoforms from the same gene when 3′ ends are distant from less than 100 nt) and 3′ intron detection. Step 6: The relative abundances of the multiple 3’UTRs generated for the same Olfr gene are assessed by RNA-Seq quantification. Rectangles: input files or output files. Diamond shapes: bash shell and perl scripts.