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
- 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
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.