Question: Bulk quality interleaving with bbmap reformat command
gravatar for infenit101
3 days ago by
infenit10110 wrote:

I have several fastq.gz files that look like this:

Sample1_R1.fastq.gz Sample1_R2.fastq.gz

Sample2_R1.fastq.gz Sample2_R2.fastq.gz


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 in=$i\_R#.fastq.gz out=$i\_interleaved.fastq.gz 

However this did not work. Can someone help me? Many Thanks!

bash bbmap bbduk loop reformat • 71 views
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