Quality control workflow

Resources

• Workshop code
• An Introduction to ShortRead (Quality control page 8)=

Quality control workflow

The ShortRead package contains a function called qa() which creates a quality report from several input formats, (usually a Fastq file).

 type=c("SolexaExport", "SolexaRealign", "Bowtie", "MAQMap", "MAQMapShort", "fastq", "BAM")

This function produces similar outputs to FastqQC but executes slightly faster. Functionality has been written to perform quality control either;

1. on a ShortReadQ structure of NGS reads loading into R using readFastq()
2. Specify the directory to run qa() directly from the NGS files.

garbageAn Introduction to ShortRead (Quality control page 8)=

Quality control workflow

The ShortRead package contains a function called qa() which creates a quality report from several input formats, (usually a Fastq file).

 type=c("SolexaExport", "SolexaRealign", "Bowtie", "MAQMap", "MAQMapShort", "fastq", "BAM")

This function produces similar outputs to FastqQC but executes slightly faster. Functionality has been written to perform quality control either;

1. on a ShortReadQ structure of NGS reads loading into R using readFastq()
2. Specify the directory to run qa() directly from the NGS files.