Folder PATH listing for volume Windows
Volume serial number is 1A53-6E1B
C:.
|   Information.txt
|   tree.txt
|   
+---Branchiostoma lanceolatum
|   |   Bl_parahox_putative_CRMs.bed
|   |   Bl_putative_CRMs.bed
|   |   vertebrate_tf_motifs_Bl_parahox_putative_CRMs.bed
|   |   
|   +---combined replicate narrowPeak files from Dr JL Skarmeta Gomez and peak gene annotations
|   |       amphi_15h_peaks.bed
|   |       amphi_36h_peaks.bed
|   |       amphi_8h_peaks.bed
|   |       peakgenes_amphi_15h_peaks.txt
|   |       peakgenes_amphi_36h_peaks.txt
|   |       peakgenes_amphi_8h_peaks.txt
|   |       
|   \---genome and annotations
|           Bl71nemr.fa
|           Bl_Annotation.gtf
|           gene_models_only_BraLan.gff3
|           
+---Comparisons
|   +---motif PCA and venn diagram input files
|   |       counts_cdx.txt
|   |       counts_lox.txt
|   |       counts_para.txt
|   |       venn_cdx.txt
|   |       venn_lox.txt
|   |       venn_para.txt
|   |       
|   \---pair wise BLAST results
|       |   bl_parahox_crms.fa
|       |   pl_parahox_crms.fa
|       |   pm_parahox_crms.fa
|       |   sp_parahox_crms.fa
|       |   
|       +---vsBl
|       |       vsBl_bl_crms.fa
|       |       vsBl_pl_crms.fa
|       |       vsBl_pm_crms.fa
|       |       vsBl_sp_crms.fa
|       |       
|       +---vsPl
|       |       vsPl_bl_crms.fa
|       |       vsPl_pl_crms.fa
|       |       vsPl_pm_crms.fa
|       |       vsPl_sp_crms.fa
|       |       
|       +---vsPm
|       |       vsPm_bl_crms.fa
|       |       vsPm_pl_crms.fa
|       |       vsPm_pm_crms.fa
|       |       vsPm_sp_crms.fa
|       |       
|       \---vsSp
|               vsSp_bl_crms.fa
|               vsSp_pl_crms.fa
|               vsSp_pm_crms.fa
|               vsSp_sp_crms.fa
|               
+---Paracentrotus lividus
|   |   Pl_parahox_putative_CRMs.bed
|   |   putative_CRMs_Pl.bed
|   |   vertebrate_tf_motifs_Pl_parahox_putative_CRMs.bed
|   |   
|   +---combined replicates narrowPeak files and peak gene annotations
|   |       peakgenes_pl_15hpf_wt.txt
|   |       peakgenes_pl_24hpf_wt.txt
|   |       peakgenes_pl_40hpf_wt.txt
|   |       pl_15hpf_wt.narrowPeak
|   |       pl_24hpf_wt.narrowPeak
|   |       pl_40hpf_wt.narrowPeak
|   |       
|   +---genome and annotations
|   |       Pliv_PqN3S_evmp.gtf
|   |       Pliv_PqN3S_sm.fa
|   |       
|   +---narrowPeak files
|   |       pl1_15hpf_wtA_peakcalling_peaks.narrowPeak
|   |       pl1_15hpf_wtB_peakcalling_peaks.narrowPeak
|   |       pl1_24hpf_wtA_peakcalling_peaks.narrowPeak
|   |       pl1_24hpf_wtB_peakcalling_peaks.narrowPeak
|   |       pl1_40hpf_wtA_peakcalling_peaks.narrowPeak
|   |       pl1_40hpf_wtB_peakcalling_peaks.narrowPeak
|   |       
|   \---peakgenes
|           all_peak_genes.narrowPeak
|           for_graph_pl.tab
|           geneswpeaks.sh
|           gene_list.txt
|           peakgenes_pl_15hpf_wt.txt
|           peakgenes_pl_24hpf_wt.txt
|           peakgenes_pl_40hpf_wt.txt
|           
+---Patiria miniata
|   |   Pm_parahox_putative_CRMs.bed
|   |   Pm_putative_CRMs.bed
|   |   vertebrate_tf_motifs_Pm_parahox_putative_CRMs.bed
|   |   
|   +---combined replicates narrowPeak files and peak gene annotations
|   |       peakgenes_pm_24hpf_wt.txt
|   |       peakgenes_pm_66hpf_wt.txt
|   |       peakgenes_pm_90hpf_wt.txt
|   |       pm_24hpf_wt.narrowPeak
|   |       pm_66hpf_wt.narrowPeak
|   |       pm_90hpf_wt.narrowPeak
|   |       
|   +---genome and annotations
|   |       genes_Pm.gtf
|   |       pmin_scaffolds_v2.0.fa
|   |       
|   \---narrowPeak files
|           pmin2_24hpf_wtA_peakcalling_peaks.narrowPeak
|           pmin2_24hpf_wtB_peakcalling_peaks.narrowPeak
|           pmin2_66hpf_wtA_peakcalling_peaks.narrowPeak
|           pmin2_66hpf_wtB_peakcalling_peaks.narrowPeak
|           pmin2_90hpf_wtA_peakcalling_peaks.narrowPeak
|           pmin2_90hpf_wtB_peakcalling_peaks.narrowPeak
|           
\---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