With attributes added, we can begin building our pipeline.

• Select the Analyses tab

In Partek Flow, data are represented as circles, termed data nodes. One data node, Unaligned reads, should be visible in the analysis tab (Figure).

• Select the Unaligned reads data node

Selecting a data node brings up a context-sensitive task menu that lists tasks that can be performed on the data node (Figure).

We will perform pre-alignment QA/QC to assess the quality of the unaligned reads and determine whether trimming or filtering is necessary. 

• Select Pre-alignment QA/QC from the QA/QC section of the task menu 
• Select Finish to run the task with default settings

Selecting a task creates a task node, e.g. the blue rectangle labeled Pre-alignment QA/QC (Figure). Selecting the task node will let us view the task report and the task details.

• Select the Pre-alignment QA/QC task node

The context-sensitive menu (Figure) shows the option to view the task report and the task details. You can also access a task report by double-clicking on a task node. 

• Select Task report

Pre-aligment QA/QC provides information about the sequencing quality of unaligned reads. Both project level summaries and sample-level summaries are provided. To view sample-level summaries, select a sample from the data table in the report. 

• Select sample SSR592573 from the data table in the report

The Average base quality score per position graph (Figure) gives the average Phred score for each position in the reads.

A Phred score is a measure of base call accuracy with a higher score indicating greater accuracy. By convention, a score above 20 is considered adequate. As we can see, the standard error bars in the graph show that some reads have quality scores below 20 for some of their base pair calls.

Based on the results of Pre-alignment QA/QC, while most of the reads are high quality, we will need to perform read trimming and filtering. 

For more information about the information included in the task report, see the Pre-aligment QA/QC User Guide. 

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