I have some ATAC-seq single cell
I know I should start with quality check of fastq files, alignment with bowtie2, sorting with samtools
I think the next is peak calling which can be done by MACS2 or Genrich
Seurat does need fragment file and raw read counts matrix
I want to ask you fragment.tsv file and raw read counts matrix are the output files of which software and which step in ATAC-seq single cell??
Google made me more confused