All samples used to generate EPDnew (hub_24769_AllCageMinus)
  Position: chr1:20,726,070-20,730,070
Total Bases in view: 4,001
Statistics on: 4,001 items covering 4,001 bases (100.00% coverage)
Average item spans 1.00 bases.
Average value -6.8163 min -2262 max 0 standard deviation 49.6459
View table schema

Go to All CAGE (-) track controls


Description

This track represents the 5′ end of PEAT reads generated by Morton et al. (2014). PEAT stands for "paired-end analysis of transcription start sites" and provides millions of TSS locations from wild-type Columbia-0 Arabidopsis thaliana whole root samples.

Methods

BAM files of mapped reads were downloaded from here and converted to BED using the "bamToBed" tool of the bedtools suite. Only the 5′-end coordinate of each read was retained, facilitating the visual identification of the putative TSS.

Credits

Data were generated Morton et al. (2014) and processed by the EPD team at the Swiss Institute of Bioinformatics (Dreos et al. 2013). For inquiries, please contact us using the on-line form here or send an e-mail to rene.dreos@sib.swiss.

References

Dreos R, Ambrosini G, Perier RC, Bucher P. EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era. Nucleic Acids Res. 2013 Jan 1;41(D1):D157-64. PMID: 23193273.

Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M. Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. The Plant Cell. 2014 Jul 1;26(7):2746-60. PMID: 25035402.