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

Description

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.

Source

Files downloaded from FTP site: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR706/ERR706688/ERR706688.fastq.gz
Input file format: FASTQ

Samples

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.

References

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

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