I have several fastq.gz files that look like this:
The output needs to be: Sample1_interleaved.fastq.gz, Sample2_interleaved.fastq.gz
I am still learning how to loop commands so bare with me. This is what I tried to run:
for i in `ls -1 *_R#.fastq.gz | sed 's/_R#.fastq.gz//‘` do reformat.sh in=$i\_R#.fastq.gz out=$i\_interleaved.fastq.gz done
However this did not work. Can someone help me? Many Thanks!