Description

This track represents the 5′ end of CAGE reads generated by Lizio et al. (2017) and is based on the FANTOM5 dataset. 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 rn6 assembly can be seen in table format here.

Methods

Raw data in BAM format was downloaded from FANTOM5. BAM files werw converted to BED using bamToBed v2.12.0 (bedtools) and to SGA using bed2sga.pl (ChIP-Seq v. 1.5.3). All tissues were merged, and the WIG file was generated with a step parameter set to 1.

Credits

Data were generated by Lizio et al. (2017) 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

Lizio M, Mukarram AK, Ohno M, Watanabe S, Itoh M, Hasegawa A, Lassmann T, Severin J, Harshbarger J, Abugessaisa I, Kasukawa T, Hon CC, Carninci P, Hayashizaki Y, Forrest ARR, Kawaji H. Monitoring transcription initiation activities in rat and dog. Sci Data. 2017 Nov 28;4:170173. doi: 10.1038/sdata.2017.173. PMID: 29182598

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