Hello

I want to parallelize a fastQC computation of a large fastq file.

I know that fastQC can be run on several files in parallel using the -t option, but I'm not sure if this will yield a correct result if I will split the file into several smaller files.

Is there any way to this?

Thanks in advance  
Dolev Rahat
If you split the files into small parts then FastQC will run on each separately and the results are not combined.

As to an answer to your question - the problem (as always) is more complicated than it looks. In a perfect world splitting the file into random subsets would produce the similar results. But splitting into random subsets is not all that easy. In addition the way FastQC works is that it some operations will only collect information from the first 200K or so reads but will then track that information throughout the file.

Often and if the data is not skewed in particular ways you can get by analyzing a small subset of the file.

In other cases (as I have painfully learned myself) subsetting a dataset can produce reports that do not even remotely resemble the original data. But that had nothing to do with the way FastQC works. 

Long story short I would run FastQC on all data then a subset of it - check if the library prep and the subject under study supports subsetting.