MiSeq quality control

Different tools and scripts to trace quality of Illumina MiSeq runs

miseq-qc.Rmd

Goal

Display quality performances of past MiSeq runs in a summary file.

Requirements

In Order to use this R Markdown script, you need to export and save the run_summary files as follows:

• on the MiSeq open Illumina Sequencing Analysis Viewer
• Browse -> select desired run folder (D:\Illumina\MiSeqOutput\yymmdd_…)
• Refresh
• in Summary tab click Copy to Clipboard...
• open Microsoft Excel
• make sure cell A1 is selected and paste values
• save as yymmdd_M02081_run_summary.xlsx in desired folder
• miseq-qc.Rmd file has to be in that same folder

Execution

Open miseq-qc.Rmd in RStudio and Knit the current document (⇧⌘K)