This directory contains the November 2004 freeze of the mouse CAGE from RIKEN, Japan. 

file descriptions.
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cage.rep_tag.*.chr_all_gff.tar.gz: Changed
	this file is tar archived all chromosome gff files. 
	please see chromosomes.

cage.all_tag.*.fasta.gz: 
	All of CAGE tag sequence file.
	this file is FASTA format.
	this sequence ID is tag_id.
	and contains tag information(rna_lib_id, rep_tag_id) in each header.

cage.rep_tag.*.fasta.gz: Changed
	representative CAGE tag sequence file.
	this file is FASTA format.
	this sequence ID is rep_tag_id.
	rep_tag_id means representative CAGE tag ID
	in clustered same CAGE tag sequence.
	and contains number of tag information in each header.

cage.rna_sample_info.*.txt.gz:
	information of rna sample using CAGE tag.
	this file is TAB separated txt as bellow:
	- rna_lib_id         : ID of rna library.
	- tissue_id          : ID of tissue type (this rule is internal).
	- dev_stage_id       : Theiler Stage.
	- tissue_name        : name of tissue type.
	- dev_stage_name     : Theiler Stage Name.
	- days_of_age        : the count of days from borned mouse.
	- time_course        : * time-coursed expriments information (optional)
	                         this time start is 01-01-2000 00:00:00(dd-MM-yyyy hh:mm:ss)
	- sample_treatment   : * sample treatment information (optional)
	- condition_name     : * experimental condition (optional)
	- cell_line_name     : * cell line name (optional)
	- collaboration_name : * collaboration name (optional)

cage.tag_info.*.txt.gz:
	information of all of CAGE tag for frequency.
	this file is TAB separated txt as bellow:
	- tag_id             : ID of CAGE tag.
	- rep_tag_id         : representative tag_id like a cluster id.
	- rna_lib_id         : ID of rna library, join for rna_sample_info.

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