FastQC-class {Repitools} | R Documentation

## 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

### Author(s)

Aaron Statham

### References

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

[Package Repitools version 1.33.3 Index]