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author | yqiancolumbia |
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date | Mon, 30 Apr 2018 05:25:11 -0400 |
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1 <tool id="getMutationType" name="Get specific types of mutations"> |
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2 <description></description> |
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3 <command interpreter="perl"> |
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4 /home/galaxy/tools/CTK/getMutationType.pl -mutationType $mutationType $input_tag_uniq_mutation_txt $output_tag_uniq_bed |
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5 </command> |
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6 |
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7 <inputs> |
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8 <param name="mutationType" type="select" label="Select a specific type of mutations "> |
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9 <option value="deletion">deletion</option> |
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10 <option value='substitution'>substitution</option> |
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11 <option value="insertion">insertion</option> |
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12 </param> |
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13 <param name="input_tag_uniq_mutation_txt" type="data" format="tabular" label="Input file in tabular format of unique mutations"/> |
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14 </inputs> |
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15 |
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16 <outputs> |
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17 <data name="output_tag_uniq_bed" format="bed" label="Get ${mutationType.value_label} mutation type on ${on_string}"> |
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18 </data> |
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19 </outputs> |
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20 |
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21 <help> |
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22 |
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23 .. class:: infomark |
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24 |
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25 **What this tool does** |
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26 |
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27 Get specific types of mutations, such as deletions, substitutions, and insertions around the cross-linked mutation site. |
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28 |
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29 ----- |
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30 |
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31 **Substitutions, deletions, and insertions** |
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32 |
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33 Based on the analysis performed so far on Nova, brPTB, Hu CLIP experiments, it appears that only deletions represent bona fide cross-linking induced mutations, while substitutions are mostly (if not all) due to sequencing/alignment errors, polymorphisms, or (potentially) RNA editing. It is estimated that ~7-25% of CLIP tags harbor deletion sites, frequently overlapping the binding motif. Therefore, it is highly recommended to do separate analysis of different types of mutations. |
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34 |
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35 However, it is not excluded that different proteins might differ due to the nature of amino-acid-nucleotide interaction and cross-linking. Therefore, analysis of more proteins will be very interesting. |
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36 |
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37 </help> |
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38 </tool> |