in wiggle format blat_mapping.py $input1 $output1

.. 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. ----- **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