Fastqc loop

Question

[camillab.]

Hi,

I want to do bulk-RNAseq so I sent to sequence 12 samples 9pair end strategy) and I need to do the fastqc, alignment etc. I am trying at the moment do to a for loop to get the fastqc since it takes ages but I am not able to do it so I am not sure what I am doing wrong.

For one sample I would do:

/Users/camilla/Desktop/FASTQ/FastQC/fastqc /Users/camilla/Desktop/FASTQ/00_fastq/P3D40_R1_001.fastq.gz —extract -o /Users/camilla/Desktop/FASTQ/QC_before

but I am not able to make it for a loop and save the output file in the folder (QC_before).

I found this code here script

for file in *.fastq
doo
echo " fastq $file"
done

but it's not really working. Can someone help me?

Thank you and apologies if it is a stupid question!

Camilla

[Ram]

Avoid that "lessons" repository - it seems to be written by a bioinformatics beginner - and not maintained at all. It also has quite a few issues that I do not wish to waste my time on. Look for answers with upvotes here or on Stack Overflow.

Answer 1

[GenoMax]

See: FastQC with multiple FASTQ files

[camillab.]

thank you! I don't know how did I not find it earlier!