Description

The subtracks represent the 5′ end of CAGE reads in 35 cell lines and are based on the dataset GSE34448. Note than only the 5′-end coordinate of each read was retained, facilitating the visual identification of the putative TSS. An overview of all the tracks provided by EPD for the hg38 assembly can be seen in table format here.

Methods

Raw data in BAM format was downloaded from UCSC. BAM files were converted to SGA format using bamToBed (SamTools) and bed2sga (ChIP-Seq v. 1.5.3). WIG files were generated with a step parameter set to 1.

Credits

Data were generated by Djebali et al. (2012) and processed by the EPD team at the Swiss Institute of Bioinformatics (Dreos et al. 2013). For inquiries, please contact us using the online form here or post a message on ask-epd@googlegroups.com.

References

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR. Landscape of transcription in human cells. Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233. PMID: 22955620

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