Merge fastqs ------------ And again, we are merging all fastq files:: cat ~/workdir/basecall/*.fastq | gzip > ~/workdir/basecall/basecall.fastq.gz cat ~/workdir/basecall_small/*.fastq | gzip > ~/workdir/basecall_small/basecall.fastq.gz If you want, you can check again for the number of reads:: zcat ~/workdir/basecall_small/basecall.fastq.gz | wc | awk '{print $1/4}' or zcat ~/workdir/basecall/basecall.fastq.gz | wc | awk '{print $1/4}'