HomeCLC FAQ - Analyses-related questionsRead mappingHow can I see all my sequences when viewing high coverage areas of a mapping?

5.4. How can I see all my sequences when viewing high coverage areas of a mapping?

Working with read mapping tracks

To see all individual reads when viewing high coverage areas, you will need to:

  • Zoom into the mapping within a region of interest.
  • Hold down the Alt key and scroll with the mouse wheel.

This will allow you to scroll down the mapped reads in the view.

You may also wish to increase the depth of the read track when viewing the read data within a mapping. To do this, place the mouse cursor in the name area of the open map track, and hover over the lower boundary of the track. You should see the cursor change to a double-headed arrow. When in that state, you can depress the left mouse button and drag the height of the track upwards or downwards.

A full list of shortcuts, including the Alt+Scroll Wheel shortcut mentioned above, can be found in our manual here:

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

 

Working with stand-alone read mapping data

To be able to scroll through all reads in a stand-alone read mapping, please choose any of the compactness levels except for the Packed option within the Read Layout section of the the side panel when working with stand-alone mapping objects.

When inspecting a read mapping, different compactness levels may be selected within the Read Layout section of the the side panel when working with stand-alone mapping objects. The default compactness level for a mapping is the Packed setting.

While all other compactness settings will stack the reads on top of each other, such that no two reads lie side by side, the Packed setting uses the available space more efficiently, allowing more reads to be seen in the same view. The benefit of this setting is a better overview when scrolling laterally through a read mapping.

However as a consequence of the organization of the Packed setting is that not necessarily all reads covering a given site are displayed. To aid with this, the vertical space used can be adjusted in the Side Panel settings in the section  Read layout | Packed read height.

To display all the reads covering a given site, you can either increase the level of Packed read height, or, you can switch from the Packed view to another compactness level, for instance Low.

Listed below are a few characteristics of the Packed setting:

  • When there are more reads than the specified packed read height allows for, a grey overflow graph will be displayed below the reads in the Packed setting.
  • When zoomed in to 100% in the Packed setting, the individual residues can be seen. But when zoomed out the reads will be represented as lines just as with the Compact setting.
  • Please note that the packed mode is special because it does not allow any editing of the read sequences and selections, and furthermore the color coding that can be specified elsewhere in the Side Panel does not take effect.

A more detailed description of the available compactness settings can be found in our online manual under this link:

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

 

Note that there is a shortcut for changing the compactness. Just press and hold the Alt key while you scroll using your mouse wheel or touchpad.

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