annotate tools/metag_tools/blat_mapping.xml @ 0:9071e359b9a3

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<tool id="blat2wig" name="Coverage of the Reads">
  <description>in wiggle format</description>
  <command interpreter="python">blat_mapping.py $input1 $output1</command>
  <inputs>	
    <param name="input1" type="data" format="tabular" label="Alignment result"/>
  </inputs>
  <outputs>
    <data name="output1" format="wig"/>
  </outputs> 
  <tests>
    <test>
      <param name="input1" value="blat_mapping_test1.txt" ftype="tabular" />
      <output name="output1" file="blat_mapping_test1.out" />
    </test>
  </tests>
  <help>

.. class:: warningmark

 To generate acceptable files, please use alignment program **BLAT** with option **-out=pslx**. 

.. class:: warningmark

 Please edit the database information by click on the pencil icon next to your dataset. Select the corresponding genome build.

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**What it does**
 
 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.

-----

**Example**

 Showing reads coverage on human chromosome 22 (partial result) in UCSC Genome Browser Custom Track:
 
 .. image:: ./static/images/blat_mapping_example.png
 	:width: 600
 	
  </help>
</tool>