

rsync -ruptl /var/www/html/rsat/perl-scripts/lib/js /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB


rsync -ruptl /var/www/html/rsat/public_html/images/program_icons/matrix-clustering_icons /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_query_matrices.transfac -from transfac -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/oct4_peak_motifs_input_motifs_processed_1.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/oct4_peak_motifs_input_motifs_processed_1.tf -from tf -to transfac -prefix_id oct4_peak_motifs -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/oct4_peak_motifs_input_motifs_processed.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/oct4_peak_motifs_input_motifs_processed.tf  > /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/input_motifs_processed.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/input_motifs_processed.tf -split -from tf -to tf -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/motif


 cat /var/www/html/rsat/R-scripts/matrix-clustering.R | /usr/bin/R --slave --no-save --no-restore --no-environ --args " infile = '/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/pairwise_compa.tab'; hclust.method = 'average'; description.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab'; distance.table = '/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/distance_table.tab'; alignment.file = '/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/alignment_table.tab'; verbosity = 0; metric = 'Ncor'; heatmap.color.palette = 'YlOrRd'; heatmap.color.classes = '9'; export.newick = 0; radial.only = 0; draw.heatmap = 1; draw.consensus = 0; pos.hclust.in.heatmap = 'column'; lthsp = 'Ncor_0.4_cor_0.6_'; out.prefix = '/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering'; "


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/cluster_1_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/cluster_1_transfac_motifs.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/cluster_2_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/cluster_2_transfac_motifs.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/cluster_3_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/cluster_3_transfac_motifs.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/input_motifs_processed.tf -from tf -to tf -matrix_id_file /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/cluster_4_motif_IDs.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_data/cluster_4_transfac_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m16_local_words_8nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m17_local_words_8nt_m2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m5_local_words_7nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m6_local_words_7nt_m2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m12_oligos_8nt_mkv6_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m13_oligos_8nt_mkv6_m2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m10_positions_7nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m5_local_words_7nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m6_local_words_7nt_m2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_3/cluster_1_node_3_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m11_positions_7nt_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m21_positions_8nt_m3_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m15_oligos_8nt_mkv6_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m12_oligos_8nt_mkv6_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m13_oligos_8nt_mkv6_m2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_2/cluster_2_node_2_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m14_oligos_8nt_mkv6_m3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m15_oligos_8nt_mkv6_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m12_oligos_8nt_mkv6_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m13_oligos_8nt_mkv6_m2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_3/cluster_2_node_3_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_3/cluster_1_node_3_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_3/cluster_1_node_3_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_cat.tf -v 0 -in_format tf -out_format tf -id cluster_2 -name cluster_2 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_cat.tf -v 0 -in_format tf -out_format tf -id cluster_3 -name cluster_3 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_2/cluster_2_node_2_cat.tf -v 0 -in_format tf -out_format tf -id cluster_2 -name cluster_2 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_2/cluster_2_node_2_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_3/cluster_2_node_3_cat.tf -v 0 -in_format tf -out_format tf -id cluster_2 -name cluster_2 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_3/cluster_2_node_3_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_2/cluster_2_nb_motifs_3.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093856_SCoPMx


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_3/cluster_1_nb_motifs_3.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093856_QG4wGt


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093856_LMDA1i


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093856_V71kca


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093856_gxSLEZ


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093856_MTGrjS


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_3/cluster_2_nb_motifs_4.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093856_kUJi8n


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_1/cluster_2_node_1_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_3/cluster_1_node_3_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_2/cluster_2_node_2_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_1/cluster_1_node_1_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_3/merged_consensuses/node_1/cluster_3_node_1_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_2/merged_consensuses/node_3/cluster_2_node_3_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_2/cluster_1_node_2_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m18_local_words_8nt_m3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m1_oligos_7nt_mkv5_m1_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_6/cluster_1_node_6_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m16_local_words_8nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m17_local_words_8nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m10_positions_7nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m5_local_words_7nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m6_local_words_7nt_m2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_4/cluster_1_node_4_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m19_positions_8nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m16_local_words_8nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m17_local_words_8nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m10_positions_7nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m5_local_words_7nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m6_local_words_7nt_m2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_5/cluster_1_node_5_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_6/cluster_1_node_6_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_6/cluster_1_node_6_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_4/cluster_1_node_4_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_4/cluster_1_node_4_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_5/cluster_1_node_5_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_5/cluster_1_node_5_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_6/cluster_1_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093857_3hgau1


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_4/cluster_1_nb_motifs_5.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093857_vNBKB6


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_5/cluster_1_nb_motifs_6.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093857_gP16XI


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_4/cluster_1_node_4_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_6/cluster_1_node_6_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_5/cluster_1_node_5_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cp /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m3_oligos_7nt_mkv5_m3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices_temp.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices_temp.tf -from tf -to tf  -attr name cluster_4 -attr accession cluster_4 -set_attr merged_AC 'oct4_peak_motifs:::oligos_7nt_mkv5_m3' -set_attr merged_ID 'oligos_7nt_mkv5_m3' -set_attr type merge -set_attr merge_type sum -set_attr merge_nb 1 -v 1 -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m7_local_words_7nt_m3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m18_local_words_8nt_m3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m1_oligos_7nt_mkv5_m1_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_7/cluster_1_node_7_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m20_positions_8nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m9_positions_7nt_m1_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_8/cluster_1_node_8_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_8/cluster_1_node_8_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_8/cluster_1_node_8_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_7/cluster_1_node_7_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_7/cluster_1_node_7_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_8/cluster_1_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093858_Hfp8Wu


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_7/cluster_1_nb_motifs_3.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093858_998DhL


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_4/cluster_4_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_8/cluster_1_node_8_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_7/cluster_1_node_7_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m22_positions_8nt_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m4_oligos_7nt_mkv5_m4_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_9/cluster_1_node_9_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m2_oligos_7nt_mkv5_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m7_local_words_7nt_m3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m18_local_words_8nt_m3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m1_oligos_7nt_mkv5_m1_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_10/cluster_1_node_10_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m8_local_words_7nt_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m19_positions_8nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m16_local_words_8nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m17_local_words_8nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m10_positions_7nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m5_local_words_7nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m6_local_words_7nt_m2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_11/cluster_1_node_11_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_9/cluster_1_node_9_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_9/cluster_1_node_9_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_10/cluster_1_node_10_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_10/cluster_1_node_10_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_11/cluster_1_node_11_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_11/cluster_1_node_11_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_9/cluster_1_nb_motifs_2.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093859_M2EO2i


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_10/cluster_1_nb_motifs_4.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093859_VF7POz


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_11/cluster_1_nb_motifs_7.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093859_FWYpeJ


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_9/cluster_1_node_9_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_11/cluster_1_node_11_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_10/cluster_1_node_10_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m22_positions_8nt_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m4_oligos_7nt_mkv5_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m8_local_words_7nt_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m19_positions_8nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m16_local_words_8nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m17_local_words_8nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m10_positions_7nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m5_local_words_7nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m6_local_words_7nt_m2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_12/cluster_1_node_12_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_12/cluster_1_node_12_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_12/cluster_1_node_12_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_12/cluster_1_nb_motifs_9.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093900_GBfmsK


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_12/cluster_1_node_12_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m2_oligos_7nt_mkv5_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m7_local_words_7nt_m3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m18_local_words_8nt_m3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m1_oligos_7nt_mkv5_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m22_positions_8nt_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m4_oligos_7nt_mkv5_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m8_local_words_7nt_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m19_positions_8nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m16_local_words_8nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m17_local_words_8nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m10_positions_7nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m5_local_words_7nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m6_local_words_7nt_m2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_13/cluster_1_node_13_cat.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m20_positions_8nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m9_positions_7nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m2_oligos_7nt_mkv5_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m7_local_words_7nt_m3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m18_local_words_8nt_m3_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m1_oligos_7nt_mkv5_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m22_positions_8nt_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m4_oligos_7nt_mkv5_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m8_local_words_7nt_m4_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m19_positions_8nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m16_local_words_8nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m17_local_words_8nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m10_positions_7nt_m2_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m5_local_words_7nt_m1_aligned.tf /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/oct4_peak_motifs_m6_local_words_7nt_m2_aligned.tf >/var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_14/cluster_1_node_14_cat.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_13/cluster_1_node_13_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_13/cluster_1_node_13_matrices.tf


/var/www/html/rsat/perl-scripts/merge-matrices -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_14/cluster_1_node_14_cat.tf -v 0 -in_format tf -out_format tf -id cluster_1 -name cluster_1 -calc sum -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_14/cluster_1_node_14_matrices.tf


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_14/cluster_1_nb_motifs_15.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093901_iKsgrm


/var/www/html/rsat/perl-scripts/convert-matrix -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_13/cluster_1_nb_motifs_13.tf -from tf -return info,header,margins -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/IC_test_2025-04-08.093901_4ayZhd


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_13/cluster_1_node_13_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


cat /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_clusters_information/cluster_1/merged_consensuses/node_14/cluster_1_node_14_trimmed_matrices.tf >> /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_aligned_logos/All_concatenated_motifs.tf


rm -r /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_pairwise_compa_logos


cp /var/www/html/rsat/public_html/templates_html/display_d3_tree.html /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_logo_tree.html


cp /var/www/html/rsat/public_html/templates_html/display_small_d3_tree.html /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_portable_logo_tree.html


mv /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_temporary.html /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_logo_tree.html


mv /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_portable_logo_tree.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/pairwise_compa_matrix_descriptions.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_html/pairwise_compa_matrix_descriptions.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/distance_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/distance_table.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/alignment_table.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/alignment_table.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/clusters.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/clusters.html


/var/www/html/rsat/perl-scripts/text-to-html -i /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/clusters_motif_names.tab -o /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_tables/clusters_motif_names.html


mv -f /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_temporary_2.html /var/www/html/rsat/public_html/tmp/www-data/2025/04/08/matrix-clustering_2025-04-08.093847_eeOvUB/matrix-clustering_portable_logo_tree.html
