Mercurial > repos > vimalkumarvelayudhan > riboplot
annotate docs/usage.rst @ 10:8964641b04ef
Fix usage link
author | Vimalkumar Velayudhan <vimal@biotechcoder.com> |
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date | Mon, 17 Aug 2015 10:51:58 +0100 |
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1 .. _usage: |
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2 |
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3 ===== |
3 | 4 Usage |
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5 ===== |
3 | 6 |
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7 RiboPlot |
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8 -------- |
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9 Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM). |
3 | 10 |
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11 Parameters |
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12 .......... |
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13 1. Ribo-Seq alignment file (Sorted BAM file) |
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14 |
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15 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM |
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16 file should be sorted. This can be done using one of the following methods. |
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17 |
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18 1. RiboGalaxy -> Sort Data -> Sort BAM dataset. |
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19 2. ``samtools sort input.bam inputsorted`` |
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20 |
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21 2. Transcriptome (FASTA) |
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22 |
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23 A FASTA format file with sequences of the transcripts. |
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24 |
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25 3. Name of the transcript to plot (Text) |
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26 |
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27 The name of the transcript to plot **should** match the name in the transcriptome (FASTA) |
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28 and the Ribo-Seq/RNA-Seq alignment (BAM). |
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29 |
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30 4. RNA coverage [optional] (Sorted BAM file) |
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31 |
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32 If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage. |
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33 |
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34 5. Read lengths to consider [Optional] (Integer - 0 or greater) |
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35 |
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36 If this option is provided, only Ribo-Seq data of the given length is considered. |
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37 |
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38 6. Offset [optional] (Integer - 0 or greater) |
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39 |
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40 If this option is provided, this offset is added to the read alignment positions. |
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41 |
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42 Output |
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43 ...... |
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44 1. Plots (PNG and SVG) |
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45 |
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46 Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue) |
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47 |
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48 RNA coverage as a gray background (if the RNA coverage option was selected). |
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49 |
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50 The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames. |
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51 |
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52 The color codes are start (white) and stop (dark gray). |
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53 |
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54 .. image:: ../images/riboplot.png |
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55 |
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56 2. RiboSeq read counts in 3 frames for each position in the transcript (CSV) |
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57 |
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58 |
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59 Command line |
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60 ............ |
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61 ``riboplot`` can also be run on the command line. The usage is :: |
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62 |
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63 usage: python riboplot.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA -t TEXT |
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64 [-n RNA_FILE] [-l INTEGER] [-s INTEGER] [-m HTML_FILE] |
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65 [-o OUTPUT_PATH] [-d] |
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66 |
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67 Plot and output read counts for a single transcript |
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68 |
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69 optional arguments: |
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70 -h, --help |
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71 show this help message and exit |
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72 |
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73 -n RNA_FILE, --rna_file RNA_FILE |
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74 RNA-Seq alignment file (BAM) |
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75 |
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76 -l INTEGER, --read_length INTEGER |
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77 Read length to consider (default: None) |
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78 |
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79 -s INTEGER, --read_offset INTEGER |
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80 Read offset (default: 0) |
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81 |
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82 -m HTML_FILE, --html_file HTML_FILE |
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83 Output file for results (HTML) |
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84 |
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85 -o OUTPUT_PATH, --output_path OUTPUT_PATH |
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86 Files are saved in this directory |
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87 |
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88 -d, --debug |
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89 Flag. Produce debug output |
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90 |
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91 required arguments: |
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92 -b RIBO_FILE, --ribo_file RIBO_FILE |
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93 Ribo-Seq alignment file in BAM format |
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94 |
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95 -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA |
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96 FASTA format file of the transcriptome |
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97 |
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98 -t TEXT, --transcript_name TEXT |
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99 Transcript name |
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100 |
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101 RiboCount |
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102 --------- |
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103 Output read counts for all transcripts in an alignment. |
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104 |
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105 Parameters |
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106 .......... |
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107 1. Ribo-Seq alignment file (Sorted BAM file) |
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108 |
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109 A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM |
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110 file should be sorted. This can be done using one of the following methods. |
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111 |
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112 1. RiboGalaxy -> Sort Data -> Sort BAM dataset. |
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113 2. ``samtools sort input.bam inputsorted`` |
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114 |
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115 2. Transcriptome (FASTA) |
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116 |
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117 A FASTA format file with sequences of the transcripts. |
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118 |
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119 3. Read lengths to consider [optional] (Integer - 0 or greater) |
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120 |
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121 If this option is provided, only Ribo-Seq data of the given length is considered. |
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122 |
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123 4. Offset [optional] (Integer - 0 or greater) |
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124 |
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125 If this option is provided, this offset is added to the read alignment positions. |
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126 |
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127 Output |
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128 ...... |
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129 Read counts for all transcripts in the alignment (ZIP) |
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130 |
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131 The output file ``ribocount_output.zip`` should first be uncompressed. This will generate |
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132 a folder called ``ribocount_output``. Open ``index.html`` in a web browser to view the results of ribocount. |
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133 |
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134 Total reads for each transcript will be displayed in a table along with the name of the transcript and a link |
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135 to the CSV file containing the read counts in 3 frames for each position in the transcript. |
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136 |
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137 .. image:: ../images/ribocount.png |
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138 |
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139 Command line |
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140 ............ |
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141 ``ribocount`` can also be run on the command line. The usage is :: |
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142 |
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143 usage: python ribocount.py [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER] |
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144 [-s INTEGER] [-m HTML_FILE] [-o OUTPUT_PATH] [-d] |
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145 |
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146 Output read counts for all transcripts |
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147 |
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148 optional arguments: |
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149 |
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150 -h, --help show this help message and exit |
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151 |
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152 -l INTEGER, --read_length INTEGER |
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153 Read length to consider (default: None) |
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154 |
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155 -s INTEGER, --read_offset INTEGER |
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156 Read offset (default: 0) |
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157 |
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158 -m HTML_FILE, --html_file HTML_FILE |
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159 |
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160 Output file for results (HTML) |
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161 |
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162 -o OUTPUT_PATH, --output_path OUTPUT_PATH |
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163 Files are saved in this directory |
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164 |
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165 -d, --debug Flag. Produce debug output |
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166 |
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167 required arguments: |
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168 |
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169 -b RIBO_FILE, --ribo_file RIBO_FILE |
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170 Ribo-Seq alignment file in BAM format |
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171 |
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172 -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA |
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173 FASTA format file of the transcriptome |
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174 |