Ngs NgsQCWizard.pdf

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Contents

NGS raw data QC wizard

Overview

The QC Wizard is a quick and easy way to run multiple QC commands simultaneously, without having to go through each individual menu. Available options are Basic statistics, Base Distribution, Quality BoxPlot, K-Mer Analysis and Sequence Duplication.

TO access this module, please select Analysis | NGS | Raw Data QC | Raw Data QC Wizard

NGS rawQC menu.png

Input Data Requirements

The "Input format" include FASTQ, QSEC, SFF, SAM, BAM and AUTO (AUTO allows the use of any combination of the listed file types).

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General Options

20130226 RawDataQC.png

Add file

Add files to menu

  • Add button will add samples by selections
  • Add Folder will add all samples in the selected folder (local project only)
  • Search will find files based on sample registration (server project only)
  • Add list will allow users to add files from a list (even add a grouping file for alignment functions).
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Options

  • Quality encoding: the user can choose Automatic (recommended) or explicitly set the quality encoding as either Illumina or Sanger.
  • Job number: The total number of samples to be run in parallel. In QC step, only one thread can read and process one sample/file. Job number is equal to ThreadNumber.The more threads that are allocated, the faster the algorithm will run. By default, this is set to the number of CPUs on the user’s computer. This should not be set to a greater number of CPUs than available, but can be reduced at the user’s discretion.
  • Zip format: Select which format is used in compressing the files (default is "None").
  • Output name: The user can choose to name the output data.
  • Output folder: Specify the folder to store the output results.
  • Generate tableland: Whether to generate tableland
  • Preview mode: will only run the module on the first 1 million reads, and should be used as a quick indicator of quality for especially large raw data files.
  • The remaining check boxes select which QC analyses to perform. The analyses include:
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Output Results

In solution explorer, several reports will be generated under "Raw Data QC" folder:

Raw data QC wizard result.png

For the detailed explanation of each result, please refer to the corresponding wiki pages.

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OmicScript

NgsQCWizard

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