Parse FASTQC data

Question

[win]

Hi all, I have a question regarding FASTQC . When we run FASTQC on FASTQ file it generates an HTML report. Is there any tool out there that can read FASTQC data, parse it and provide it in raw form. I need this so that I could use the values in an algorithm to determine if the data is of good quality.

Any help will be highly appreciated.

[Pierre Lindenbaum]

isn't there usually a txt file associated with this html page ? e.g: https://github.com/ChillarAnand/fadapa/blob/master/tests/fastqc_data.txt

[Matteo Schiavinato]

If I remember correctly, it is printed out only if you specify an --outdir.

Answer 1

[James Ashmore]

By default FastQC should generate a zip folder with files containing the data used for plotting.

[GenoMax]

This is the right answer .. at least when fastq is run on the command line (e.g. fastqc file.fq.gz file2.fq.fz). I don't recollect if you run fastqc using the GUI this works.

Answer 2

[Matteo Schiavinato]

Specify an --outdir and all the output files will be placed there, including a txt report that you can easily parse, and the html file that you can open to see the results in a graphical-friendly format. The two files contain the same information.

[pcsk9]

there is now a tool available to parse the output of fastqc into a python dictionary, which can then be converted into pandas dataframes for downstream aggregation and querying

https://pypi.org/project/fastqcparser/