FastQC and associated classes

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Description

The FastQC class stores results obtained from the FastQC application (see references), with a slot for each FastQC module. The SequenceQC class contains the QC results of a single lane of sequencing in three slots: Unaligned - FastQC results obtained from all reads (before alignment) Aligned - FastQC results obtained from only reads which aligned Mismatches - a data.frame containing counts for the number of mismatches of each type found at each sequencing cycle

Slots of a FastQC object

Basic_Statistics

Per_base_sequence_quality

Per_sequence_quality_scores

Per_base_sequence_content

Per_base_GC_content

Per_sequence_GC_content

Per_base_N_content

Sequence_Length_Distribution

Sequence_Duplication_Levels

Overrepresented_sequences

Slots of a SequenceQC object

Unaligned - FastQC results obtained from all reads (before alignment)

Aligned - FastQC results obtained from only reads which aligned

Mismatches - a data.frame containing counts for the number of mismatches of each type found at each sequencing cycle

MismatchTable - a data.frame containing counts of how many mismatches aligned sequences contain

Author(s)

Aaron Statham

References

FastQC - http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

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