Folder PATH listing for volume Windows
Volume serial number is 1A53-6E1B
C:.

\---Strongylocentrotus purpuratus
    |   Sp_parahox_putative_CRMs.bed
    |   Sp_putative_CRMs.bed
    |   Sp_tfs_in_parahox_CRMs_hindgut_72hpf.bed
    |   vertebrate_tf_motifs_Sp_parahox_putative_CRMs.bed
    |   
    +---combined replicate narrowPeak files and peak gene annotations
    |       peakgenes_sp_24hpf_wt.txt
    |       peakgenes_sp_48hpf_gut.txt
    |       peakgenes_sp_48hpf_wt.txt
    |       peakgenes_sp_66hpf_gut.txt
    |       peakgenes_sp_66hpf_wt.txt
    |       peakgenes_sp_72hpf_wt.txt
    |       sp_24hpf_wt.narrowPeak
    |       sp_48hpf_gut.narrowPeak
    |       sp_48hpf_wt.narrowPeak
    |       sp_66hpf_gut.narrowPeak
    |       sp_66hpf_wt.narrowPeak
    |       sp_72hpf_wt.narrowPeak
    |       
    +---differential analysis
    |   |   named_48_RNA_UP_ATAC_UP.txt
    |   |   named_66_RNA_UP_ATAC_UP.txt
    |   |   
    |   +---ATAC-seq
    |   |   +---48hpf
    |   |   |       denovo_homerResults_48hpf_atac_gut_more_open.html
    |   |   |       loci_sp48_atac_gut_DN.bed
    |   |   |       loci_sp48_atac_gut_UP.bed
    |   |   |       sp48_ATAC_gut_wt.tsv
    |   |   |       
    |   |   \---66hpf
    |   |           denovo_homerResults_66hpf_gut_more_open.html
    |   |           loci_sp66_atac_gut_DN.bed
    |   |           loci_sp66_atac_gut_UP.bed
    |   |           sp66_ATAC_gut_wt.tsv
    |   |           
    |   \---RNA-seq
    |           annotated_Sp48hpf_gut_wt_RUV.csv
    |           annotated_Sp66hpf_gut_wt_RUV.csv
    |           annotated_Sp_gut66_gut48_RUV.csv
    |           
    +---genome and annotations
    |   |   SPU_function.txt
    |   |   SPU_GO.txt
    |   |   SPU_PFAM.txt
    |   |   WHL_names_table.txt
    |   |   WHL_NCBI.txt
    |   |   WHL_SPU.txt
    |   |   
    |   +---S. purpuratus genome 3.1
    |   |       Spur_3.1.LinearScaffold.fa
    |   |       Transcriptome.gtf
    |   |       
    |   \---S.purpuratus genome 5.0
    |           spur5.fasta
    |           SPU_ids_on_spur5.gff3
    |           
    +---HiC data
    |   +---100kb resolution
    |   |       chr11.mat
    |   |       chr11_xgi.bed
    |   |       sample1_100000.matrix
    |   |       sample1_100000_abs.bed
    |   |       
    |   \---20kb resolution ParaHox on target analysis
    |           parahox_norm.mat
    |           parahox_norm_xgi.bed
    |           sample1_ontarget_20000.matrix
    |           sample1_ontarget_20000_abs.bed
    |           Sp_50hpf_pairs.txt
    |           Sp_50hpf_significant_20000.txt
    |           
    +---known CRMs
    |       known_CRMs_TFs_check.txt
    |       known_CRM_sea_urchin.xlsx
    |       
    +---narrowPeak files
    |       sp4_24hpf_wtA_peakcalling_peaks.narrowPeak
    |       sp4_24hpf_wtB_peakcalling_peaks.narrowPeak
    |       sp4_48hpf_gutA_peakcalling_peaks.narrowPeak
    |       sp4_48hpf_gutB_peakcalling_peaks.narrowPeak
    |       sp4_48hpf_wtA_peakcalling_peaks.narrowPeak
    |       sp4_48hpf_wtB_peakcalling_peaks.narrowPeak
    |       sp4_66hpf_gutA_peakcalling_peaks.narrowPeak
    |       sp4_66hpf_gutB_peakcalling_peaks.narrowPeak
    |       sp4_66hpf_wtA_peakcalling_peaks.narrowPeak
    |       sp4_66hpf_wtB_peakcalling_peaks.narrowPeak
    |       sp4_72hpf_wtA_peakcalling_peaks.narrowPeak
    |       sp4_72hpf_wtB_peakcalling_peaks.narrowPeak
    |       
    \---scRNAseq
            sp72_positive_genes_annotated_all_clusters.xlsx
            sp72_tf_info_all_clusters.xlsx