# FANTOM6 raw data directory

The directory contains FANTOM6 raw files, mainly,
FASTQ, mapping BAM and CTSS files.

The directory structure is as follows:

## top directory

Each targeted cell samples (types) is numbered as "SetXX" (e.g. Set1, Set2, ..),
and their analyzed data is put in each subdirectory ("SetXX_XXXXX").

## subdirectories

### CAGE

CAGE/
	Files related to CAGE libraries
CAGE/SetXX_Ref/
	Files obtained in each (reference) CAGE run
CAGE/SetXX_RunXX/
	Files obtained in each (perturbed) CAGE run (in trasfection RunXX)

CAGE/SetXX_XXX/seqs/
	FASTQ files
CAGE/SetXX_XXX/tophat_mapping/
	mapped BAM files (using tophat program)
CAGE/SetXX_XXX/tophat_ctss/
	CTSS BED files (using tophat program)


### directional RNA-Seq

directional_RNA_Seq/
	Files related to directional RNA-Seq
directional_RNA_Seq/SetXX_Fractionation/
	Files obtained by the fractionation experiment.

directional_RNA_Seq/SetXX_XXX/seqs/
	FASTQ files
directional_RNA_Seq/SetXX_XXX/tophat_mapping/
	mapped BAM files (using tophat program)


### RNA-Seq

The files in this directory was used to target gene selection
of Set1 (human dermal fibroblast).
Only FASTQ files are available.



### Hi-C

Hi-C/
	Files related to Hi-C
Hi-C/SetXX_Ref/
	Files obtained in each (reference) Hi-C run

Hi-C/SetXX_XXX/seqs/
	FASTQ files


### ChIRP-Seq

ChIPP_Seq/
	Files related to ChIRP-Seq
ChIRP_Seq/SetXX_Ref/
	Files obtained in each (reference) ChIRP-Seq run

ChIRP_Seq/SetXX_XXX/seqs/
	FASTQ files