I have a folder structure with multiple fastq files in different directories.
Is there a way to run fastqc on all the fastq files in the different directories with just one command?
I have tried it with
find . -name "*.fq" | fastqc -
but it didn't work.
thanks in advance
I like a similar (but maybe simpler?) version of this using
And if your filenames have spaces in them, it works fine with:
My files are not zipped, so I used the first option. But I get an error massage:
removed the dash after fastqc
This won't work, as it will open the interactive windows of the fastqc program (x11).
sorry, I was reasoning with cutadapt not fastqc. Try to read /dev/stdin.
I think I figure it out thanks to your Idea. I just changed
now it's running. I still need to see if it runs all over the files. but at least it works.
Thanks for the advice