10.5281/zenodo.545682
https://zenodo.org/records/545682
oai:zenodo.org:545682
Kawaji, Hideya
Hideya
Kawaji
Preventive medicine and applied genomics unit, RIKEN Advanced Center for Computing and Communication
Transcription initiation peaks based on FANTOM5 CAGE data on hg38 and mm10
Zenodo
2017
fantom5
fantom
transcriptome
transcription starting sites
TSS
genomics
computational biology
2017-04-12
Creative Commons Attribution 4.0 International
Overview
Decomposition-based peak identification (DPI, https://github.com/hkawaji/dpi1) is applied to the re-processed (re-aligned) FANTOM5 data, upon hg38 (GRCh38) and mm10 (GRCm38), obtained from below:
http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v1/basic/
http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v1/basic/
The same parameters to the ones used in the previous paper (Forrest ARR, Kawaji H, Rehli M, et al. Nature 507: 462–470, 2014) was used.
Data files
Four data files per assembly are prepared as below.
tag cluster in the original definition (*.tc.bed.gz)
full set of DPI peaks (*.tc.decompose_smoothing_merged.bed.gz)
permissive set of DPI peaks (*.tc.decompose_smoothing_merged.ctssMaxCounts3.bed.gz)
robust set of DPI peaks (*.tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.bed.gz)
Acknowledgement
This data set is supported by Research Grant from MEXT to RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Center for Life Science Technologies, and JSPS KAKENHI Grant-in-Aid for Scientific Research No. 16H02902.