Deep sequencing-based cap analysis of gene expression (DeepCAGE) to investigate the transcription start sites (TSS) of genes in wild type S. pombe grown in normal conditions.
Raw data was downloaded from EBI ArrayExpress database (ID E-MTAB-3188) and mapped to spo2 genome using Bowtie aligner. Note that 1 base was trimmed from the 5' end of each sequence to account for a mis-alignment of 1 bp between CAGE tags and the Initiator motif. The resulting SAM files were converted to BED using SAMtools and BEDtools. Final conversion to SGA files was done using ChIP-Seq.
Li H, Hou J, Bai L, Hu C, Tong P, Kang Y, Zhao X, Shao Z. Genome-wide Analysis of Core Promoter Structures in Schizosaccharomyces pombe with DeepCAGE RNA Biology [2015, 12(5):525-537]. PubMed PMID: 25747261