Description

These tracks represent 5′ end of CAGE reads from all cell lines merged 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 hg19 assembly can be seen in table format here.

Methods

Raw data in BAM format was downloaded from UCSC. BAM file were converted to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3). After a close inspection of the peak generated by these files, it appared clear that they were shifted of 1 nucleotide. In fact, Init element was not center at position 0 as expected but at position -1. All the tags were then shifted accordingly to overcame this inconsistency. The WIG files were generated with a step parameter set to 1.

Credits

Data was 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

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