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41 lines
1.4 KiB
XML
41 lines
1.4 KiB
XML
<tool id="Interval2Bed1" name="Interval2Bed">
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<description>creates a Bed query for displaying at UCSC</description>
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<command interpreter="perl">Text2BedLike.pl $input_chromCol $input_startCol $input_endCol $input_strandCol $input $out_file1</command>
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<inputs>
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<param format="Interval" name="input" type="data" label="In Query"/>
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</inputs>
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<outputs>
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<data format="bed" name="out_file1" />
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</outputs>
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<help>
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**Interval2Bed** can be used convert Interval query into Bed query for dislaying at UCSC Genome Browser
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-----
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**Example**
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You want to convert the following data into BED::
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2 - 478789 477812 TEF1/YPR080W
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1 - 73302 72328 CDC19/YAL038W
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4 + 1347867 1348565 SSN2/YDR443C
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7 - 373310 372735 RCS1/YGL071W
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Running Text2Bed will generate::
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chr2 478789 477812 BedLike|2|-|478789|477812|TEF1/YPR080W 0 -
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chr1 73302 72328 BedLike|1|-|73302|72328|CDC19/YAL038W 0 -
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chr4 1347867 1348565 BedLike|4|+|1347867|1348565|SSN2/YDR443C 0 +
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chr7 373310 372735 BedLike|4|+|1347867|1348565|SSN2/YDR443C 0 -
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The BED like data above contain all necessary BED fields: *chromosome*, *start*, *end*, *name*, *score* and *strand*.
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Note that all original information is preserved and packed within *name* field (column 4).
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.. class:: infomark
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**TIP:** To restore original data use **BedLike2Text** tool in *Convert Formats->BedLike2text*
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</help>
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</tool> |