Quality control is performed by using FastQC. Because data quality may differ between forward and reverse sets of paired-end reads, they are displayed separately.


The left frame will show the set clicked on at the upload page (otherwise R1), the right frame the other set. In some browsers (such as Chrome) the hyperlinks under Summary of both FastQC Reports will quickly take you to the according sections of both (vertically aligned) frames. Other browsers (Firefox) need the frames to be opened in separate tabs/windows (right-click on the frame, this frame, open frame in new tab) in order for these links to work. This also offers the opportunities to save the reports in HTML format.


For further computations, however, one might want to export the pure numbers without the charts. "Show me the numbers" above each frame yields a tab-delimited text that can be saved and imported by spreatsheet programs such as Excel or OpenOffice or computing environments such as R or Matlab.

Computational Steps

(Warning: For bioinformaticians only. If you wonder if Hidden Markov is something for Russian children to find on Easter morning you may want to skip this.)

Ref. Genome: NC_000962.3
FastQC v0.10.1