CAGE Track Settings
 
Selected FANTOM CAGE samples

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Track height: pixels (range: 11 to 128)
Data view scaling: Always include zero: 
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Windowing function: Smoothing window:  pixels
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 Select all subtracks
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dense
 Configure 		 (+)MesenchymalStemCells  Mesenchymal Stem Cells, Bone Marrow Derived, plus strand   Data format 
dense
 Configure 		 (+)Hepatocytes  Hepatocytes, plus strand   Data format 
dense
 Configure 		 (+)AorticSmoothMusc  Aortic Smooth Muscle Cells, plus strand   Data format 
dense
 Configure 		 (+)AorticSmoothMuscDiff  Aortic Smooth Muscle Cells, Differentiated, plus strand   Data format 
dense
 Configure 		 (-)MesenchymalStemCells  Mesenchymal Stem Cells, Bone Marrow Derived, minus strand   Data format 
dense
 Configure 		 (-)Hepatocytes  Hepatocytes, minus strand   Data format 
dense
 Configure 		 (-)AorticSmoothMusc  Aortic Smooth Muscle Cells, minus strand   Data format 
dense
 Configure 		 (-)AorticSmoothMuscDiff  Aortic Smooth Muscle Cells, Differentiated, minus strand   Data format 
    

Description

The subtracks represent the 5′ end of CAGE reads generated by Lizio et al. (2017) and are 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 canFam3 assembly can be seen in table format here.

Methods

Raw data in BAM format was downloaded from FANTOM5. BAM files were converted to BED using bamToBed v2.12.0 ( bedtools) and to SGA using bed2sga.pl (ChIP-Seq v. 1.5.3). WIG files were 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