Repitools (version 1.14.0)

FastQC-class: FastQC and associated classes

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

References

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