Counting sequences in many fasta or fastq files

[calderatta]

I'm trying to find read counts for each of the fastq files that I have. Right now, I'm using grep on the @ character but I'm not sure how to do this for multiple files.

[sr320]

Here is some useful code: https://github.com/RobertsLab/code/blob/master/fasta.md

I think this code for fastq for fastq files: awk '{s++}END{print s/4}' file.fastq via https://www.biostars.org/p/139006/

I normally just use fastQC output to know number of reads.

using a for loop something like

%%bash
for f in /where/your/files/r/*fq
do
awk '{s++}END{print s/4}' $f
done

[kubu4]

grep can process a list of files.

Here's an example for fastq files:

grep -c '@' *.fq

This will search for the @ symbol in any files ending with .fq and will print the filename and the number of results for each file.

[kubu4]

"Pro" tip -

Most FastQ files comes compressed as gzip files.

Use zgrep -c '@' *.fq.gz to search through compressed FastQ files.