HomeCLC FAQ - Analyses-related questionsRead mappingHow can I export the coverage for each position in my mapping?

5.7. How can I export the coverage for each position in my mapping?

There are two options for exporting coverage values for every position of a reference.

Export Mapping Coverage

Available for: Genomics Workbench 7, Main Workbench 7, Biomedical Genomics Workbench 2.1 and later versions of these workbenches.

Input: Read mapping tracks, stand-alone read mappings and mapping graph tracks.

Description: This export option sends detailed coverage information to a Tab Separate Values (.tsv) file.

To export the detailed coverage information use the File | Export menu, the Export button from the Workbench toolbar, or right-click on the input file in your navigation area and select Export. Select the Mapping Coverage as export format. A description of the information exported using this tool is provided in our manual here:

http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Read_mapping_formats.html

 

Export just coverage values to comma separate text file

Available for: All CLC Workbenches that support read mappings.

Input: Stand-alone read mappings. (Not read mapping tracks.)

Description: This route leads to the generation of a comma delimited text file containing the coverage values for every position of a reference in a stand-alone read mapping object.

How to do this is described in our manual here:

http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Export_graph_data_points_file.html#sec:exportgraphincsvformat

If you cannot see the coverage graph in your stand-alone read mapping, then please check the viewing settings in the right hand panel of the Workbench. The Graph setting is described in our manual on this page in the *Alignment Info* section:

http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Mapping_view_settings.html

If you are working with a track-based mapping, please consider using the export tool and choosing the Mapping coverage option, as described above, instead.

If you really want to use the option described here to get a file containing coverage values for a read mapping track, then you must first convert it to a stand-alone object using the Convert From Tracks tool found at:

Toolbox | Track Tools | Convert From Tracks


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