total beginner trying to learn about quality control

Question

[brianhughes26]

I have fastqc reports for 40 variants. Is there a quick way to combine the basic statistics onto a spreadsheet?

[Joe]

I vaguely recall that FastQC May output some plaintext files you could probably parse in to a table... I may be totally wrong though.

[cschu181]

It does. By default, FastQC creates a directory with text output in addition to the .html. One can choose the --noextract option to keep that directory as a zipped archive.

Answer 1

[Philipp Bayer]

Would MultiQC be fine? However, it makes a new HTML file summarising all input reports, I don't think it can make a CSV

[cschu181]

I'm fairly sure you can export the report tables.