Question: total beginner trying to learn about quality control
0
gravatar for brianhughes26
3 months ago by
brianhughes260 wrote:

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

next-gen • 183 views
ADD COMMENTlink modified 3 months ago by Philipp Bayer5.9k • written 3 months ago by brianhughes260

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

ADD REPLYlink written 3 months ago by jrj.healey10k

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.

ADD REPLYlink written 3 months ago by cschu1811.5k
2
gravatar for Philipp Bayer
3 months ago by
Philipp Bayer5.9k
Australia/Perth/UWA
Philipp Bayer5.9k wrote:

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

ADD COMMENTlink written 3 months ago by Philipp Bayer5.9k

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

ADD REPLYlink written 3 months ago by cschu1811.5k
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