cmd = novel_PD75_ATAC-seq_peaks_in_last_half_of_gene_at_least_3500bp_from_RefSeq_TSS_new.bed hg19 Motifs_3 -size 300 -mask -preparsedDir Motifs_3/PP -bg background_novel_ATAC_seq_peaks_in_last_half_of_gene_new.bed