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.



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

RNA-seq data:

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

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


Last update: 2 Oct 2017