QC

This module calls fastqc, a quality check program, to analyze the quality of each sample.

By default, creates a final MultiQC report with all the samples. It is useful to check if there are outliers among the input samples. It can be disabled using the option --skip_report.

How to run the QC module

Executing the following:

XICRA QC -h

The different options and parameters for this module should appear in the command line prompt:

Module XICRA QC help
Parameters

--help (-h) – Show this help message and exit.

Module XICRA QC Input/Output
Parameters

  • --input – Folder containing the files with reads. Files could be .fastq/.fq/ or fastq.gz/.fq.gz. See --help_format for additional details. REQUIRED.

  • --output_folder – Output folder. Name for the project folder.

  • --batch – Provide this option if input is a file containing multiple paths instead a path.

  • --in_sample – File containing a list of samples to include (one per line) from input folder(s). Default OFF.

  • --ex_sample – File containing a list of samples to exclude (one per line) from input folder(s). Default OFF.

  • --detached – Isolated mode. No project folder initiated for further steps. Default OFF.

  • --include_lane – Include the lane tag (L00X) in the sample identification. See --help_format for additional details. Default OFF.

  • --include_all – Include all file name characters in the sample identification. See --help_format for additional details. Default OFF.

Module XICRA QC options
Parameters

  • --skip_report – Do not report statistics using MultiQC report module. Default OFF.

  • --threads – Number of CPUs to use. Default: 2.

Module XICRA QC additional information
Parameters

  • --help_format – Show additional help on name format for files.

  • --help_project – Show additional help on the project scheme.

  • --help_multiqc – Show additional help on the multiQC module.

  • --debug – Show additional message for debugging purposes.

  • For further information of the module functionallity, check this page.

Output of QC

After the QC module excution,in the data folder for each sample, a new directory will be created. It will be called ‘fastq’ and will contain the the quality analysis.

In addition, if --skip_report was not selected, a folder called ‘report’ will also be generated. In this folder, the different reports that may be created after the execution of other modules (as trimm) will be stored. These reports will always show information of all the samples. In this case, a subfolder called ‘fastqc’ will be built with the MultiQC report in order to visualize the quality analysis of all samples.