sc-DIRECTORY.md

The directory structure of input and output folders

A schematic view of the data structure for the typical single-cell data analysis

+ fastq_directory (INPUT)
+ workdir         (OUTPUT)
    ++ sc_trimmed
    ++ sc_trimmed2
    ++ sc_log
	+++ trim
	+++ bowtie2
	+++ bamSort
	+++ bamMarkdup
    ++ sc_aligned.aug10
	+++ sorted
	+++ dup.marked
	+++ dup.marked.clean
    ++ sc_countMatrix
    ++ sc_cluster
    ++ sc_qc
	+++ report
	+++ figure
    ++ sc_pseudoBulk
	+++ groups_aggregation
	    ++++ single_cells
	    ++++ pseudo_bulk_data
		+++++  macs2
		+++++  SEACR
	+++ group_1
	    ++++ single_cells
	    ++++ pseudo_bulk_data
	    	+++++  macs2
		+++++  SEACR
	+++ group_2
	    ++++ single_cells
	    ++++ pseudo_bulk_data
	    	+++++  macs2
		+++++  SEACR