Determine %bases >=Q30 for individual samples

[cheezemeister]

Illumina Sequencing Analysis Viewer only seems to report the % bases >= Q30 for the entire run. Is there a quick and easy way for me to determine this metric for each individual sample from the FASTQ files? FastQC doesn't seem to output this metric.

[GenoMax]

You can use bbduk.sh from BBMap to get a ball park idea (this will miss some bases < Q30 if they are inside the leftover read).

$ bbduk.sh in=sample.fastq.gz trimq=30 qtrim=rl

[kmcarr]

Did you run bcl2fastq to demultiplex the lane? If so then locate the file Demultiplex_Stats.htm, which is under the "Basecall_Stats_<flowcellID>/" subdirectory of the bcl2fastq output directory. You can open this up in any web browser. For each demultiplexed sample it shows the % ≥ Q30, Average Q Score and a number of other metrics.

[cheezemeister]

Did you run bcl2fastq to demultiplex the lane? If so then locate the file Demultiplex_Stats.htm, which is under the "Basecall_Stats_<flowcellID>/" subdirectory of the bcl2fastq output directory. You can open this up in any web browser. For each demultiplexed sample it shows the % ≥ Q30, Average Q Score and a number of other metrics.

The lane was demultiplexed by the MiSeq software; it wasn't done manually by me.

[Brian Bushnell]

I just added a new flag to Reformat for calculating this. Usage:

reformat.sh in=reads.fq qchist=qchist.txt

That stands for "quality count histogram".