Transcription initiation peaks based on FANTOM5 CAGE data on rn6, canFam3, and galGal5

Overview

Decomposition-based peak identification (DPI, https://github.com/hkawaji/dpi1) is applied to the FANTOM5 data of rat (rn3), dog (canFam3), and chicken (galGal5):

https://fantom.gsc.riken.jp/5/datafiles/phase2.6/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 Integrative Medical Sciences, and JSPS KAKENHI Grant-in-Aid for Scientific Research No. 16H02902.