[2] | 1 | <tool id="blat2wig" name="Coverage of the Reads"> |
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| 2 | <description>in wiggle format</description> |
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| 3 | <command interpreter="python">blat_mapping.py $input1 $output1</command> |
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| 4 | <inputs> |
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| 5 | <param name="input1" type="data" format="tabular" label="Alignment result"/> |
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| 6 | </inputs> |
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| 7 | <outputs> |
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| 8 | <data name="output1" format="wig"/> |
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| 9 | </outputs> |
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| 10 | <tests> |
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| 11 | <test> |
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| 12 | <param name="input1" value="blat_mapping_test1.txt" ftype="tabular" /> |
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| 13 | <output name="output1" file="blat_mapping_test1.out" /> |
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| 14 | </test> |
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| 15 | </tests> |
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| 16 | <help> |
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| 17 | |
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| 18 | .. class:: warningmark |
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| 19 | |
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| 20 | To generate acceptable files, please use alignment program **BLAT** with option **-out=pslx**. |
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| 21 | |
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| 22 | .. class:: warningmark |
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| 23 | |
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| 24 | Please edit the database information by click on the pencil icon next to your dataset. Select the corresponding genome build. |
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| 25 | |
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| 26 | ----- |
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| 27 | |
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| 28 | **What it does** |
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| 29 | |
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| 30 | This tool takes **BLAT pslx** output and returns a wig-like file showing the number of reads (coverage) mapped at each chromosome location. Use **Graph/Display Data --> Build custom track** tool to show the coverage mapping in UCSC Genome Browser. |
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| 31 | |
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| 32 | ----- |
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| 33 | |
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| 34 | **Example** |
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| 35 | |
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| 36 | Showing reads coverage on human chromosome 22 (partial result) in UCSC Genome Browser Custom Track: |
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| 37 | |
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| 38 | .. image:: ../static/images/blat_mapping_example.png |
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| 39 | :width: 600 |
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| 40 | |
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| 41 | </help> |
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| 42 | </tool> |
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