Li 2015, Genome-wide Analysis of TSS of S. pombe using DeepGAGE


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.


Files downloaded from FTP site:
Input file format: FASTQ


From Pombe 2004 (spo2) Assembly

Technical Notes

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

Genome browser viewable files