fastQC output question

[arrchi]

Hi there,

Here is one of the reports from fastQC. In the per_base_quality plot, the first 11 bases look weird. I wonder if I need to trim the first 11 bases? And possible reasons?

Thank a bunch.

[JQL]

mine look quite similar to yours. So I have same questions.
The QC suggests it passed. I wonder what is the recommended passing score? 30? what standard they use to make the pass/fail call?

thanks

Hi there,

Here is one of the reports from fastQC. In the per_base_quality plot, the first 11 bases look weird. I wonder if I need to trim the first 11 bases? And possible reasons?

Thank a bunch.

[kmcarr]

arrchi,

Your plot is a perfectly normal (and good) plot for Illumina HiSeq data. For whatever reason the Q-score prediction algorithm in the HiSeq RTA stair steps the quality scores over the first 13 bases (3-5-5).