view tools/metag_tools/blat_mapping.xml @ 1:cdcb0ce84a1b

author xuebing
date Fri, 09 Mar 2012 19:45:15 -0500
parents 9071e359b9a3
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<tool id="blat2wig" name="Coverage of the Reads">
  <description>in wiggle format</description>
  <command interpreter="python"> $input1 $output1</command>
    <param name="input1" type="data" format="tabular" label="Alignment result"/>
    <data name="output1" format="wig"/>
      <param name="input1" value="blat_mapping_test1.txt" ftype="tabular" />
      <output name="output1" file="blat_mapping_test1.out" />

.. 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.

**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.



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