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1 #+TITLE: TAREAN output description
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2 #+HTML_HEAD_EXTRA: <link rel="stylesheet" type="text/css" href="style1.css" />
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3 #+LANGUAGE: en
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4
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5 * Introduction
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6 TAREAN output includes *HTML report* with list of all analyzed clusters; the clusters are classified into five categories:
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7 + high confidence satellites
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8 + low confidence satellites
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9 + potential LTR elements
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10 + rDNA
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11 + other clusters
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12 Each cluster for which consensus sequences was reconstructed has also its own detailed report, linked to the main report.
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13
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14 * Main HTML report
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15 This report contains basic information about all clusters larger than specified threshold (default value is 0.01% of analyzed reads)
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16 ** Table legend
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17 + Cluster :: Cluster identifier
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18 + Genome Proportion[%] :: /(Number of sequences in cluster/Number of sequences in clustering) x 100%/
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19 + Size :: Number of reads in the cluster
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20 + Satellite probability :: Empirical probability estimate that cluster sequences
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21 are derived from satellite repeat. This estimate is based on analysis of more
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22 than xxx clusters including yyy manually anotated and zzz experimentaly
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23 validated satellite repeats
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24 + Consensus :: Consensus sequence is outcome of kmer-based
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25 analysis and represents the most probable satellite monomer
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26 sequence
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27 + Kmer analysis ::
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28 link to analysis report for individual clusters
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29 + Graph layout :: Graph-based visualization of similarities among sequence
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30 reads
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31 + Connected component index :: Proportion of nodes of the graph which are part
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32 of the the largest strongly connected component
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33 + Pair completeness index :: Proportion of reads with available
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34 mate-pair within the same cluster
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35 + Kmer coverage :: Sum of relative frequencies of all kmers used for consensus
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36 sequence reconstruction
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37 + |V| :: Number of vertices of the graph
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38 + |E| :: Number of edges of the graph
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39 + PBS score :: Primer binding site detection score
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40 + The longest ORF length :: Length of the longest open reading frame found in
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41 any of the possible six reading frames. Search was done on dimer of
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42 consensus so ORFs can be longer than 'monomer' length
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43 + Similarity-based annotation :: Annotation based on
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44 similarity search using blastn/blastx against database of known
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45 repeats.
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46 * Detailed cluster report
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47 Cluster report includes a list of major monomer sequence varinats reconstructed from the most frequent k-mers. The reconstructed consensus sequences are sorted based on their significance (that is, what proportion of k-mer they represent).
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48 ** Table legend
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49 - kmer :: length of kmer used for consensus reconstruction.
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50 - variant :: identifier of consensus variant.
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51 - total score :: measure of significance of consensus variant. Score is calculated as a sum of weights of all k-mers used for consensus reconstruction.
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52 - monomer length :: length of the consensus
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53 - consensus :: consensus sequence without ambiguous bases.
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54 - graph image :: part of de-Bruijn graph based on the abundant k-mers. Size of
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55 vertices corresponds to k-mer frequencies, Paths in the graph which was used
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56 for reconstruction of consensus sequences is gray colored.
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57 - logo image :: consensus sequences shown as DNA logo. Height of letters corresponds to kmer frequencies. Logo images are linked to corresponding position probability matrices.
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58
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59 * Structure of the output archive
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60 Complete results from TAREAN analysis can by downloaded as zip archive which contains the following
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61 files and directories:
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62
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63 #+BEGIN_SRC files & directories
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64 .
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65 .
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66 ├── clusters_info.csv <------------ list of clusters in tab delimited format
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67 ├── index.html <------------ main html report
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68 ├── seqclust
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69 │ ├── assembly # not implemented yet
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70 │ ├── blastn <------------ results of read comparison with DNA database
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71 │ ├── blastx <------------ results of read comparison with protein database
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72 │ ├── clustering
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73 │ │ ├── clusters
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74 │ │ │ ├── dir_CL0001 <----┐- detailed information about clusters
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75 │ │ │ ├── dir_CL0002 <----│
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76 │ │ │ ├── dir_CL0003 <----│
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77 │ │ │ .... <----┘
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78 │ │ │
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79 │ │ └── hitsort.cls <--------- list of reads in individual clusters
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80 │ ├── mgblast
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81 │ ├── prerun
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82 │ └── sequences <--------- input reads
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83 ├── summary # not implemented yet
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84 ├── TR_consensus_rank_1_.fasta <-- reconstructed monomer sequences for HIGH confidence satellites
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85 ├── TR_consensus_rank_2_.fasta <-- reconstructed monomer sequences for LOW confidence satellites
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86 ├── TR_consensus_rank_3_.fasta <-- reconstructed sequences of potential LTR elements
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87 └── TR_consensus_rank_4_.fasta <-- reconstructed consensus for rDNA
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88
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89 #+END_SRC
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90
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91 List of all clusters which is available in HTML file =index.html= is also
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92 available in tab delimited format in the file =clusters_info.csv= which can be
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93 easily viewed and edited in spreadsheet editing programs. List of all clusters
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94 and the corresponding reads is in the file =hitsort.cls= which has the following
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95 format:
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96
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97 : >CL1 11
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98 : 134234r 55494f 85525f 136746r 96742f 91926f 239729r 105445f 222518r 136402r 9013
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99 : >CL2 10
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100 : 76205r 120735r 69527r 12235r 176778f 189307f 131952f 163507f 100038r 178475r
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101 : >CL3 6
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102 : 99835r 222598f 29715r 102023f 99524r 30116f
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103 : >CL4 6
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104 : 51723r 69073r 218774r 146425f 136314r 41744f
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105 : >CL5 5
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106 : 70686f 65565f 234078r 50430r 68247r
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107
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108 where =CL1 11= is the cluster ID followed by number of reads in the cluster;
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109 next line contains list of all read names belonging to the cluster.
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110 ** structure of cluster directories
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111
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112 Detailed information for each cluster is stored is subdirectories:
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113
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114 #+BEGIN_SRC folder directories
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115 dir_CL0011
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116 ├── blast.csv <------------tab delimited file, all-to-all comparison od reads within cluster
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117 ├── CL11_directed_graph.RData <----directed graph representation of cluster saved as R igraph object
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118 ├── CL11.GL <-----------------undirected graph representation of cluster saved as R igraph object
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119 ├── CL11.png <-----------┐- images with graph visualization
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120 ├── CL11_tmb.png <-----------┘
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121 ├── dna_database_annotation.csv <-- annotation of cluster reads based on the DNA database of repeats
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122 ├── reads_all.fas <---------------- all reads included in the cluster in fasta format
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123 ├── reads.fas <---------------- subset of reads used for monomer reconstruction
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124 ├── reads_oriented.fas <------------ subset of reads all in the same orientation
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125 └── tarean
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126 ├── consensus.fasta <----------- fasta file with tandem repeat consensus variants
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127 ├── ggmin.RData
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128 ├── img
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129 │ ├── graph_11mer_1.png <-----┐
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130 │ ├── graph_11mer_2.png <-----│
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131 │ ├── graph_15mer_2.png <-----│
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132 │ ├── graph_15mer_3.png <-----│
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133 │ ├── graph_15mer_4.png <-----│ images of kmer-based graphs used for reconstruction of
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134 │ ├── graph_19mer_2.png <-----│ monomer variants
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135 │ ├── graph_19mer_4.png <-----│
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136 │ ├── graph_19mer_5.png <-----│
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137 │ ├── graph_23mer_2.png <-----│
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138 │ ├── graph_27mer_3.png <-----┘
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139 │ │
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140 │ ├── logo_11mer_1.png <-----┐
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141 │ ├── logo_11mer_2.png <-----│
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142 │ ├── logo_15mer_2.png <-----│
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143 │ ├── logo_15mer_3.png <-----│
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144 │ ├── logo_15mer_4.png <-----│ images with DNA logos representing consensus sequences
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145 │ ├── logo_19mer_2.png <-----│ of monomer variants
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146 │ ├── logo_19mer_4.png <-----│
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147 │ ├── logo_19mer_5.png <-----│
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148 │ ├── logo_23mer_2.png <-----│
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149 │ └── logo_27mer_3.png <-----┘
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150 │
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151 ├── ppm_11mer_1.csv <-----┐
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152 ├── ppm_11mer_2.csv <-----│
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153 ├── ppm_15mer_2.csv <-----│
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154 ├── ppm_15mer_3.csv <-----│
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155 ├── ppm_15mer_4.csv <-----│ position probability matrices for individual monomer
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156 ├── ppm_19mer_2.csv <-----│ variants derived from k-mer frequencies
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157 ├── ppm_19mer_4.csv <-----│
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158 ├── ppm_19mer_5.csv <-----│
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159 ├── ppm_23mer_2.csv <-----│
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160 ├── ppm_27mer_3.csv <-----┘
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161 │
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162 ├── reads_oriented.fas_11.kmers <-----┐
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163 ├── reads_oriented.fas_15.kmers <-----│
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164 ├── reads_oriented.fas_19.kmers <-----│ k-mer frequencies calculated on oriented reads
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165 ├── reads_oriented.fas_23.kmers <-----│ for k-mer lengths 11 - 27
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166 ├── reads_oriented.fas_27.kmers <-----┘
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167 ├── reads_oriented.fasblast_out.cvs <---------┐results of blastn search against database of tRNA
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168 ├── reads_oriented.fasblast_out.cvs_L.csv <----│for purposes of LTR detection
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169 ├── reads_oriented.fasblast_out.cvs_R.csv <----┘
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170 └── report.html <--- cluster analysisHTML summary
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171 #+END_SRC
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