Input data format

ATAC-seq

Supported formats	Description	Required tags	Optional tags	Note
*.fastq or *.fastq.gz	Raw reads	None	None
*.bam	Aligned reads	None	“filtered”: do not further filter this file
*.bed or *.bed.gz	Aligned reads	None		Paired reads need to be provided as the 3-column BEDPE format used by MACS2

RNA-seq

Supported formats	Description	Required tags	Optional tags
*.fastq or *.fastq.gz	Raw reads	None	None
Plain Text	Expression profile	“gene quantification”	None

HiC

Supported formats	Description	Required tags	Optional tags
Plain Text	a list of Loops	“loops”	None

Taiji can automatically download data from ENCODE portal and GEO database.