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.

• Raw data was downloaded from FTP site
• Input file format: FASTQ

From S. pombe (Aug 2015 ASM294v2/spo2).

Transcription Profiling data:

	Filename	Description	Feature	GEO-ID
1	ERR706688.sga	DeepCAGE for TSS mapping	DeepCAGE	-

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. SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).

• 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 Biol. 2015;12(5):525-37. doi: 10.1080/15476286.2015.1022704. 25747261