2014-11-11
Marina Lizio (marina.lizio@riken.jp)
Inquiries to fantom-help@gsc.riken.jp

Clustering of CAGE TSS following DPI method (kawaji@gsc.riken.jp)
This folder contains CAGE peaks expression tables for the robust (expression>10TPM) set of peaks.

Description of the columns in CAGE peaks coordinates files:
chromosome
start of CAGE peak region
end of CAGE peak region
name (ID) of the CAGE peak
score (NOTE: this does NOT correspond to the totals of reads in all samples, please do NOT use it as expression value)
strand of the CAGE peak
start of the representative TSS position
end of the representative TSS position (Note: end is always start+1)
rgb string for color coding (plus or minus strand only)

hg19.cage_peak_phase1and2combined_coord.bed.gz - CAGE peaks coordinates for human samples
hg19.cage_peak_phase1and2combined_ann.txt.gz - CAGE peak based table with annotated peaks for human samples
hg19.cage_peak_phase1and2combined_tpm.osc.txt.gz - CAGE peak based expression table (RLE normalized) for human samples [see edgeR documentation for further details about normalization method]
hg19.cage_peak_phase1and2combined_counts.osc.txt.gz - CAGE peak based expression table for human samples
hg19.cage_peak_phase1and2combined_tpm_ann.osc.txt.gz - CAGE peak based expression table (RLE normalized) for human with annotation
hg19.cage_peak_phase1and2combined_counts_ann.osc.txt.gz - CAGE peak based expression table for human with annotation
hg19.cage_peak_phase1and2combined_relative_expr.txt.gz - CAGE peak based relative expression (log10 expression relative to median) for human
mm9.cage_peak_phase1and2combined_ann.txt.gz - CAGE peak based table with annotated peaks for mouse samples
mm9.cage_peak_phase1and2combined_coord.bed.gz - CAGE peaks coordinates for mouse samples
mm9.cage_peak_phase1and2combined_tpm.osc.txt.gz - CAGE peak based expression table (RLE normalized) for mouse samples
mm9.cage_peak_phase1and2combined_counts.osc.txt.gz - CAGE peak based expression table for mouse samples
mm9.cage_peak_phase1and2combined_tpm_ann.osc.txt.gz - CAGE peak based expression table (RLE normalized) for mouse with annotation
mm9.cage_peak_phase1and2combined_counts_ann.osc.txt.gz - CAGE peak based expression table for mouse with annotation
mm9.cage_peak_phase1and2combined_relative_expr.txt.gz - CAGE peak based relative expression (log10 expression relative to median) for mouse