Genome-wide Analysis of Core Promoter Structures in Schizosaccharomyces pombe with DeepCAGE

We used a deep sequencing-based cap analysis of gene expression (DeepCAGE) to generate 16 million uniquely mapped tags, corresponding to 93,736 positions on the genome of the fission yeast. Deep sequencing of the CAGE library generated 20,115,604 CAGE tags, and these tags were mapped to the S. pombe genome (Ensembl Genomes fungi release-12) using Bowtie. With two mismatches allowed in Bowtie, 16,028,846 (79.7%) tags were uniquely mapped while 2,819,094 (14.0%) tags were mapped to multiple locations. Tags mapped to rRNA genes accounted for <8.5% of all CAGE tags, indicating the high quality of our CAGE library.