Understanding the Bowtie Map configuration

After the bowtie-pp2.xml configuration file has been imported, click the CLC bio Bowtie Map name to see the configuration (figure 12.17).

Image external_app_bowtie_thin_client
Figure 12.17: The External command tab of the CLC bio Bowtie Map configuration is visible in the external application editor.

From an end-user perspective, when the configuration on the CLC Server is complete, they will be able to launch the CLC bio Bowtie Map tool via their Workbench Toolbox. A wizard will appear, within which they will select the sequencing reads to be mapped, identify the pre-built index file of the reference sequence to use and set a few parameters. The bowtie executable will then be executed on the server system and the results generated will be imported into the CLC Server using post processing tools. The sam mapping file is imported using the Import SAM/BAM Mapping Files tool. A fasta file of sequences mapping to multiple locations is imported using the Fasta High-Throughput Sequencing Import tool.

Below, we step through the General configuration panel and then explain the configuration of the post processing tools that handle the outputs from the bowtie analysis.

General configuration panel

Each of the parameters (items within curly brackets) written into the "Command line" box is presented as an item in the General configuration panel. There, we define the type of information each parameter expects or represents and default values, where relevant.

To understand how these parameters relate to the information that will be passed to the native bowtie executable, please refer to the bowtie_map.sh script in the clcbio folder that should now be in place in the bowtie distribution folder.

Stepping through the parameters in the order they appear in the Command line area of the configuration, and thus the order they appear in the General config panel:

Post processing - importing the results from Bowtie

If you expand click on the High-throughput sequencing import /Post-processing link below the General configuration area, you will see that there are two post-processing tools selected: the Import SAM/BAM Mapping Files tool and the Fasta High-Throughput Sequencing Import tool.

In each case, clicking on the Edit and map paramaters button below it will bring up the configuration window for that tool. Here, several types of configuration can be carried out.

  1. Mapping of outputs of the external application to inputs of the post processing tool.
  2. Locking or unlocking of parameters, determining which parameters users can alter when launching the tool via the Workbench or Command Line Tools.
  3. Setting default values for parameters of the external application.

Here, we step through the configuration of the Import SAM/BAM Mapping Files tool. The configuration of the Fasta High-Throughput Sequencing Import is similar.

The parameters in this configuration window are the Import SAM/BAM Mapping Files tool parameters, just as would be offered when that tool is launched directly in a CLC Workbench.

A locked lock symbol by a parameter means that the user will not be given access to this option when launching the tool. Default settings for lock parameters are used. The locked parameters shown in figure 12.18 indicate that a track will be output rather than a stand-alone read mapping, unmapped reads will be saved, references will not be downloaded from an external source and, had they been, downloaded references will not be saved. Quality scores and sequence names will be kept (not discarded).

By contrast, the References parameter is unlocked. When using the Import SAM/BAM Mapping Files tool, users need to specify where the relevant reference sequences are. Thus, this option should be made available for users to configure when the tool is being launched.

The input to the Import SAM/BAM Mapping Files also needs to be defined. This is done by mapping the relevant output from the bowtie command to the input parameter for the Import SAM/BAM Mapping Files tool. The output from bowtie is defined by the "sam file" parameter, and the relevant input parameter in the import tool is "Selected files". A drop down list of potentially relevant parameters appears to the left of the "Selected files" parameter. In our example, this has already been mapped to the "sam file" parameter of the command, as shown in figure 12.18.

Image bowtie2
Figure 12.18: Configuration of Import SAM/BAM Mapping Files for import of a sam file after mapping using Bowtie.

Note: The drop-down lists of possibly relevant parameters provided in the post processing tool configuration window are populated based only on the types of parameters (in the General config pane). Any parameters of a type that could be relevant are presented. This means that some parameters appearing in these lists may not make sense contextually.